Centre for Bioinformatics and Computational Biology - User contributions [en]

http://wiki.bi.up.ac.za/wiki/api.php?action=feedcontributions&feedformat=atom&user=Fourie Centre for Bioinformatics and Computational Biology - User contributions [en] 2026-04-04T06:47:50Z User contributions MediaWiki 1.23.13 http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2026-01-30T10:25:27Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture is available [https://docs.google.com/spreadsheets/d/1VXVs3ShJHie-XD2D3S2YWGqAkM9lnmqx3mrPHLYd6nM here].<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> * [http://wiki.bi.up.ac.za/home Admin Wiki]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Obtaining_an_account Obtaining an account 2025-03-18T10:29:48Z

<p>Fourie: </p> <hr /> <div>There are two main types of accounts:<br /> * A Linux server login account (terminal-based). This is the default account type. You'll definitely need one of these.<br /> * A Galaxy web-based account (more information about Galaxy is available [https://galaxyproject.org here]). If you don't know what Galaxy is, you'll probably not need one of these.<br /> To apply for an account, please fill in the [https://docs.google.com/forms/d/e/1FAIpQLSeDkEtYQB83tHOVcoYKgNzq9gngW9674MoMf6EEJlfI29oVNw/viewform?usp=header Account Application Form].</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2025-02-19T12:13:51Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture is available [https://docs.google.com/spreadsheets/d/1Jg5edGbH-p5Kp9XiD9twD7GpzCPjjdTVby4fn6-Ms34 here].<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> * [http://wiki.bi.up.ac.za/home Admin Wiki]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2025-02-19T12:12:59Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1Jg5edGbH-p5Kp9XiD9twD7GpzCPjjdTVby4fn6-Ms34 schedule] is currently available only to bioinformatics students, due to COVID social distancing restrictions.<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> * [http://wiki.bi.up.ac.za/home Admin Wiki]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2024-11-18T13:49:24Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://app.globus.org Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type "CBCB" and look for "UP CBCB" at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server. '''Underneath the password field, choose Advanced and set a credential lifetime in hours.''' Once logged in, you will be able to see your files at UP<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be "CHPC South Africa - Lengau" if you would like to connect to the CHPC (first e-mail helpdesk@chpc.ac.za to get your Globus ID linked to your CHPC login name). <br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2024-11-18T13:48:53Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://app.globus.org Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type "CBCB" and look for "UP CBCB" at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server. '''Underneath the password field, choose Advanced and set a credential lifetime in hours.''' Once logged in, you will be able to see your files at UP<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be "CHPC South Africa - Lengau" if you would like to connect to the CHPC (first e-mail helpdesk@chp.ac.za to get your Globus ID linked to your CHPC login name). <br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2024-11-18T13:47:58Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://app.globus.org Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type "CBCB" and look for "UP CBCB" at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server. '''Underneath the password field, choose Advanced and set a credential lifetime in hours.''' Once logged in, you will be able to see your files at UP<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC South Africa - Lengau if you would like to connect to the CHPC (first e-mail helpdesk@chp.ac.za to get your Globus ID linked to your CHPC login name). <br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2023-02-07T09:58:39Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1EQQ9lTBi-Pyr6PKgq4eTak-0CU5y52Zg7jJ3LiNyfZQ/edit#gid=0 schedule] is currently available only to bioinformatics students, due to COVID social distancing restrictions.<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> * [http://wiki.bi.up.ac.za/home Admin Wiki]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2021-09-28T22:43:05Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://app.globus.org Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server. '''Underneath the password field, choose Advanced and set a credential lifetime in hours.''' Once logged in, you will be able to see your files at UP<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2021-09-28T22:42:00Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://app.globus.org Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server. Underneath the password field, choose Advanced and set a credential lifetime in hours. Once logged in, you will be able to see your files at UP<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2021-02-01T13:40:05Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1mNpNbf6D752dAP3mVNYhEeVvXAcDzigRQVVCbCbwq5Q/edit#gid=0 schedule] is currently available only to bioinformatics students, due to COVID social distancing restrictions.<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2021-02-01T13:37:34Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1mNpNbf6D752dAP3mVNYhEeVvXAcDzigRQVVCbCbwq5Q/edit#gid=0 schedule] is available for any interested students from other departments to attend. Lectures are on Mondays at 11:00 and Wednesdays at 11:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2020-10-13T02:03:23Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://app.globus.org Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2020-03-05T04:02:29Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Mondays at 11:00 and Wednesdays at 11:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2020-02-18T06:23:00Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [http://linuxcommand.org/tlcl.php The Linux Command Line ]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays at 10:00 and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2020-02-18T06:21:59Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * The Linux Command Line [http://linuxcommand.org/tlcl.php]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays at 10:00 and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == The Black Mamba ==<br /> * [[About]]<br /> * [[Joining the discussion]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2019-07-17T11:52:48Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays at 10:00 and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == The Black Mamba Resource ==<br /> * [[Joining the discussion]]<br /> * [[Python]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2019-06-18T13:30:53Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays at 11:00 and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> == [[The Black Mamba Resource]] ==</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2019-06-18T13:26:45Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays at 11:00 and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]<br /> * [[The Black Mamba Resource]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2019-02-19T10:59:46Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays at 11:00 and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2019-02-08T13:39:33Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2019-02-08T13:39:13Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture https://docs.google.com/spreadsheets/d/1DYL-XHFb4-o3mi6E6x1F4kLRCdFKrdLERI7LO6RqwbI/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]<br /> * [[File and directory permissions and ownership]]<br /> * [[Guidelines and Terms of use]]<br /> * [[Safety and security at the Lab]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Using_the_PBS_/_Torque_queueing_environment Using the PBS / Torque queueing environment 2018-09-14T07:22:16Z

<p>Fourie: </p> <hr /> <div>The main commands for interacting with the Torque environment are:<br /> <br /> <source lang="c"><br /> > qstat<br /> </source><br /> View queued jobs.<br /> <br /> <br /> <source lang="c"><br /> > qsub<br /> </source><br /> Submit a job to the scheduler.<br /> <br /> <br /> <source lang="c"><br /> > qdel<br /> </source><br /> Delete one of your jobs from queue.<br /> <br /> <br /> === Job script parameters ===<br /> <br /> Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:<br /> <br /> <source lang="c"><br /> #PBS -l nodes=1:ppn=14<br /> </source><br /> <br /> sets the size of the job in number of processors:<br /> <br /> nodes=N sets the number of nodes needed.<br /> <br /> ppn=N sets the number of cores per node.<br /> <br /> <source lang="c"><br /> #PBS -l walltime=8:00:00<br /> </source><br /> <br /> sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.<br /> <br /> <br /> === Example job scripts ===<br /> <br /> A program using 14 cores on a single node:<br /> <br /> <source lang="c"><br /> #!/bin/bash<br /> #PBS -l nodes=1:ppn=14<br /> #PBS -l walltime=8:00:00<br /> #PBS -q normal<br /> #PBS -o /path/to/stdout.log<br /> #PBS -e /path/to/stderr.log<br /> #PBS -k oe<br /> #PBS -m ae<br /> #PBS -M your.email@address<br /> <br /> module load bowtie2-2.3.4.1<br /> bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam<br /> </source><br /> <br /> <br /> Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is:<br /> <br /> <source lang="c"><br /> > qsub run_bowtie.sh<br /> </source><br /> <br /> If you receive an email with exit status "0", that would usually indicate that the job completed successfully.<br /> <br /> === Interactive jobs ===<br /> <br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> <br /> === The different queues available ===<br /> <br /> <br /> {| class="wikitable"<br /> !Queue Name<br /> !Max user jobs running <br /> !Max user cores <br /> running per job<br /> !Max memory<br /> !Max walltime<br /> !Description <br /> |-<br /> |short<br /> |6<br /> |28<br /> |128 GB<br /> |00:05:00<br /> |Short queue with 5 minute time limit<br /> |-<br /> |normal<br /> |4<br /> |28<br /> |128 GB<br /> |08:00:00<br /> |Medium queue with 8 hour time limit<br /> |-<br /> |long<br /> |1<br /> |28<br /> |128 GB<br /> |168:00:00<br /> |Long queue with one week time limit<br /> |-<br /> |bigmem<br /> |1<br /> |24<br /> |750 GB<br /> |72:00:00<br /> |High memory queue with 3 day time limit<br /> |-<br /> |mpi<br /> |1<br /> |112<br /> |128 GB<br /> |72:00:00<br /> |Queue for mpi parallel jobs with 3 day time limit<br /> |}<br /> <br /> * If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.<br /> ** Both MPICH and openMPI are installed. Please select the relevant environment using the "module load" functionality.<br /> ** The node list for MPI can be accessed as $PBS_NODEFILE.<br /> <br /> === Additional information ===<br /> <br /> * A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].<br /> * Detailed reference documentation for queue submission is available [http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm here].</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2018-07-31T07:41:29Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=unspecified&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1cPluvAnTzm9Wx-RFeisVo_OPFDMWoXWFdmySA4wEitg/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays and Thursdays at 10:00 in FABI Square 3-26<br /> * [[Migrating your data safely]]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-06-07T12:56:27Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 2,000 per year.<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://storageadmin.bi.up.ac.za http://storageadmin.bi.up.ac.za].<br /> * nLustre quotas can also be checked with:<br /> <source lang="c"><br /> > lfs quota -u username /nlustre<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account (R 2,000 per year) provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** 5 TB total (add 4)<br /> ** 10 TB<br /> ** 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-06-07T12:55:56Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 2,000 per year.<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://storageadmin.bi.up.ac.za http://storageadmin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > lfs quota -u username /nlustre<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account (R 2,000 per year) provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** 5 TB total (add 4)<br /> ** 10 TB<br /> ** 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-06-07T12:55:44Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 2,000 per year (to be confirmed soon).<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://storageadmin.bi.up.ac.za http://storageadmin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > lfs quota -u username /nlustre<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account (R 2,000 per year) provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** 5 TB total (add 4)<br /> ** 10 TB<br /> ** 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-06-07T12:55:23Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 1,500 per year (to be confirmed soon).<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://storageadmin.bi.up.ac.za http://storageadmin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > lfs quota -u username /nlustre<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account (R 2,000 per year) provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** 5 TB total (add 4)<br /> ** 10 TB<br /> ** 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Using_the_PBS_/_Torque_queueing_environment Using the PBS / Torque queueing environment 2018-05-31T19:54:35Z

<p>Fourie: </p> <hr /> <div>The main commands for interacting with the Torque environment are:<br /> <br /> <source lang="c"><br /> > qstat<br /> </source><br /> View queued jobs.<br /> <br /> <br /> <source lang="c"><br /> > qsub<br /> </source><br /> Submit a job to the scheduler.<br /> <br /> <br /> <source lang="c"><br /> > qdel<br /> </source><br /> Delete one of your jobs from queue.<br /> <br /> <br /> === Job script parameters ===<br /> <br /> Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:<br /> <br /> <source lang="c"><br /> #PBS -l nodes=1:ppn=14<br /> </source><br /> <br /> sets the size of the job in number of processors:<br /> <br /> nodes=N sets the number of nodes needed.<br /> <br /> ppn=N sets the number of cores per node.<br /> <br /> <source lang="c"><br /> #PBS -l walltime=8:00:00<br /> </source><br /> <br /> sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.<br /> <br /> <br /> === Example job scripts ===<br /> <br /> A program using 14 cores on a single node:<br /> <br /> <source lang="c"><br /> #!/bin/bash<br /> #PBS -l nodes=1:ppn=14<br /> #PBS -l walltime=8:00:00<br /> #PBS -q normal<br /> #PBS -o /path/to/stdout.log<br /> #PBS -e /path/to/stderr.log<br /> #PBS -m ae<br /> #PBS -M your.email@address<br /> <br /> module load bowtie2-2.3.4.1<br /> bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam<br /> </source><br /> <br /> <br /> Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is:<br /> <br /> <source lang="c"><br /> > qsub run_bowtie.sh<br /> </source><br /> <br /> <br /> === Interactive jobs ===<br /> <br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> <br /> === The different queues available ===<br /> <br /> <br /> {| class="wikitable"<br /> !Queue Name<br /> !Max user jobs running <br /> !Max user cores <br /> running per job<br /> !Max memory<br /> !Max walltime<br /> !Description <br /> |-<br /> |short<br /> |6<br /> |28<br /> |128 GB<br /> |00:05:00<br /> |Short queue with 5 minute time limit<br /> |-<br /> |normal<br /> |4<br /> |28<br /> |128 GB<br /> |08:00:00<br /> |Medium queue with 8 hour time limit<br /> |-<br /> |long<br /> |1<br /> |28<br /> |128 GB<br /> |168:00:00<br /> |Long queue with one week time limit<br /> |-<br /> |bigmem<br /> |1<br /> |24<br /> |750 GB<br /> |72:00:00<br /> |High memory queue with 3 day time limit<br /> |-<br /> |mpi<br /> |1<br /> |112<br /> |128 GB<br /> |72:00:00<br /> |Queue for mpi parallel jobs with 3 day time limit<br /> |}<br /> <br /> * If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.<br /> ** Both MPICH and openMPI are installed. Please select the relevant environment using the "module load" functionality.<br /> ** The node list for MPI can be accessed as $PBS_NODEFILE.<br /> <br /> === Additional information ===<br /> <br /> * A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].<br /> * Detailed reference documentation for queue submission is available [http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm here].</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Running_jobs_on_our_servers Running jobs on our servers 2018-05-31T19:52:42Z

<p>Fourie: </p> <hr /> <div>* You cannot run jobs directly on the head node or computre servers, you should use the [http://wiki.bi.up.ac.za/wiki/index.php?title=Using_the_PBS_/_Torque_queueing_environment Torque / PBS queue environment] to run your jobs.<br /> ** If for some exceptional reason you need to run a job directly on one of the servers (e.g. a job using a Linux GUI environment, please discuss your needs with our system administrator (johann.swart at up.ac.za).<br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> <br /> * If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Running_jobs_on_our_servers Running jobs on our servers 2018-05-31T19:52:30Z

<p>Fourie: </p> <hr /> <div>* You cannot run jobs directly on the head node or computre servers, you should use the [http://wiki.bi.up.ac.za/wiki/index.php?title=Using_the_PBS_/_Torque_queueing_environment Torque / PBS queue environment] to run your jobs.<br /> ** If for some exceptional reason you need to run a job directly on one of the servers (e.g. a job using a Linux GUI environment, please discuss your needs with our system administrator (johann.swart at up.ac.za).<br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> * If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Using_the_PBS_/_Torque_queueing_environment Using the PBS / Torque queueing environment 2018-05-31T19:51:46Z

<p>Fourie: </p> <hr /> <div>The main commands for interacting with the Torque environment are:<br /> <br /> <source lang="c"><br /> > qstat<br /> </source><br /> View queued jobs.<br /> <br /> <br /> <source lang="c"><br /> > qsub<br /> </source><br /> Submit a job to the scheduler.<br /> <br /> <br /> <source lang="c"><br /> > qdel<br /> </source><br /> Delete one of your jobs from queue.<br /> <br /> <br /> === Job script parameters ===<br /> <br /> Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:<br /> <br /> <source lang="c"><br /> #PBS -l nodes=1:ppn=14<br /> </source><br /> <br /> sets the size of the job in number of processors:<br /> <br /> nodes=N sets the number of nodes needed.<br /> <br /> ppn=N sets the number of cores per node.<br /> <br /> <source lang="c"><br /> #PBS -l walltime=8:00:00<br /> </source><br /> <br /> sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.<br /> <br /> <br /> === Example job scripts ===<br /> <br /> A program using 14 cores on a single node:<br /> <br /> <source lang="c"><br /> #!/bin/bash<br /> #PBS -l nodes=1:ppn=14<br /> #PBS -l walltime=8:00:00<br /> #PBS -q normal<br /> #PBS -o /path/to/stdout.log<br /> #PBS -e /path/to/stderr.log<br /> #PBS -m ae<br /> #PBS -M your.email@address<br /> <br /> module load bowtie2-2.3.4.1<br /> bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam<br /> </source><br /> <br /> <br /> Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is:<br /> <br /> <source lang="c"><br /> > qsub run_bowtie.sh<br /> </source><br /> <br /> <br /> === Interactive jobs ===<br /> <br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> <br /> === The different queues available ===<br /> <br /> <br /> {| class="wikitable"<br /> !Queue Name<br /> !Max user jobs running <br /> !Max user cores <br /> running per job<br /> !Max memory<br /> !Max walltime<br /> !Description <br /> |-<br /> |short<br /> |6<br /> |28<br /> |128 GB<br /> |00:05:00<br /> |Short queue with 5 minute time limit<br /> |-<br /> |normal<br /> |4<br /> |28<br /> |128 GB<br /> |08:00:00<br /> |Medium queue with 8 hour time limit<br /> |-<br /> |long<br /> |1<br /> |28<br /> |128 GB<br /> |168:00:00<br /> |Long queue with one week time limit<br /> |-<br /> |bigmem<br /> |1<br /> |24<br /> |750 GB<br /> |72:00:00<br /> |High memory queue with 3 day time limit<br /> |-<br /> |mpi<br /> |1<br /> |112<br /> |128 GB<br /> |72:00:00<br /> |Queue for mpi parallel jobs with 3 day time limit<br /> |}<br /> <br /> * If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.<br /> <br /> === Additional information ===<br /> <br /> * A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].<br /> * Detailed reference documentation for queue submission is available [http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm here].</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Using_the_PBS_/_Torque_queueing_environment Using the PBS / Torque queueing environment 2018-05-31T19:51:00Z

<p>Fourie: </p> <hr /> <div>The main commands for interacting with the Torque environment are:<br /> <br /> <source lang="c"><br /> > qstat<br /> </source><br /> View queued jobs.<br /> <br /> <br /> <source lang="c"><br /> > qsub<br /> </source><br /> Submit a job to the scheduler.<br /> <br /> <br /> <source lang="c"><br /> > qdel<br /> </source><br /> Delete one of your jobs from queue.<br /> <br /> <br /> === Job script parameters ===<br /> <br /> Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:<br /> <br /> <source lang="c"><br /> #PBS -l nodes=1:ppn=14<br /> </source><br /> <br /> sets the size of the job in number of processors:<br /> <br /> nodes=N sets the number of nodes needed.<br /> <br /> ppn=N sets the number of cores per node.<br /> <br /> <source lang="c"><br /> #PBS -l walltime=8:00:00<br /> </source><br /> <br /> sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.<br /> <br /> <br /> === Example job scripts ===<br /> <br /> A program using 14 cores on a single node:<br /> <br /> <source lang="c"><br /> #!/bin/bash<br /> #PBS -l nodes=1:ppn=14<br /> #PBS -l walltime=8:00:00<br /> #PBS -q normal<br /> #PBS -o /path/to/stdout.log<br /> #PBS -e /path/to/stderr.log<br /> #PBS -m ae<br /> #PBS -M your.email@address<br /> <br /> module load bowtie2-2.3.4.1<br /> bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam<br /> </source><br /> <br /> <br /> Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is:<br /> <br /> <source lang="c"><br /> > qsub run_bowtie.sh<br /> </source><br /> <br /> <br /> === Interactive jobs ===<br /> <br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> <br /> === The different queues available ===<br /> <br /> <br /> {| class="wikitable"<br /> !Queue Name<br /> !Max user jobs running <br /> !Max user cores <br /> running per job<br /> !Max memory<br /> !Max walltime<br /> !Description <br /> |-<br /> |short<br /> |6<br /> |28<br /> |128 GB<br /> |00:05:00<br /> |Short queue with 5 minute time limit<br /> |-<br /> |normal<br /> |4<br /> |28<br /> |128 GB<br /> |08:00:00<br /> |Medium queue with 8 hour time limit<br /> |-<br /> |long<br /> |1<br /> |28<br /> |128 GB<br /> |168:00:00<br /> |Long queue with one week time limit<br /> |-<br /> |bigmem<br /> |1<br /> |24<br /> |750 GB<br /> |72:00:00<br /> |High memory queue with 3 day time limit<br /> |-<br /> |#mpi<br /> |1<br /> |112<br /> |128 GB<br /> |72:00:00<br /> |Queue for mpi parallel jobs with 3 day time limit<br /> |}<br /> <br /> \# If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.<br /> <br /> === Additional information ===<br /> <br /> * A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].<br /> * Detailed reference documentation for queue submission is available [http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm here].</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Using_the_PBS_/_Torque_queueing_environment Using the PBS / Torque queueing environment 2018-05-31T19:50:35Z

<p>Fourie: </p> <hr /> <div>The main commands for interacting with the Torque environment are:<br /> <br /> <source lang="c"><br /> > qstat<br /> </source><br /> View queued jobs.<br /> <br /> <br /> <source lang="c"><br /> > qsub<br /> </source><br /> Submit a job to the scheduler.<br /> <br /> <br /> <source lang="c"><br /> > qdel<br /> </source><br /> Delete one of your jobs from queue.<br /> <br /> <br /> === Job script parameters ===<br /> <br /> Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:<br /> <br /> <source lang="c"><br /> #PBS -l nodes=1:ppn=14<br /> </source><br /> <br /> sets the size of the job in number of processors:<br /> <br /> nodes=N sets the number of nodes needed.<br /> <br /> ppn=N sets the number of cores per node.<br /> <br /> <source lang="c"><br /> #PBS -l walltime=8:00:00<br /> </source><br /> <br /> sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.<br /> <br /> <br /> === Example job scripts ===<br /> <br /> A program using 14 cores on a single node:<br /> <br /> <source lang="c"><br /> #!/bin/bash<br /> #PBS -l nodes=1:ppn=14<br /> #PBS -l walltime=8:00:00<br /> #PBS -q normal<br /> #PBS -o /path/to/stdout.log<br /> #PBS -e /path/to/stderr.log<br /> #PBS -m ae<br /> #PBS -M your.email@address<br /> <br /> module load bowtie2-2.3.4.1<br /> bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam<br /> </source><br /> <br /> <br /> Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is:<br /> <br /> <source lang="c"><br /> > qsub run_bowtie.sh<br /> </source><br /> <br /> <br /> === Interactive jobs ===<br /> <br /> * If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:<br /> <br /> <br /> <source lang="c"><br /> > qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00<br /> </source><br /> <br /> <br /> === The different queues available ===<br /> <br /> <br /> {| class="wikitable"<br /> !Queue Name<br /> !Max user jobs running <br /> !Max user cores <br /> running per job<br /> !Max memory<br /> !Max walltime<br /> !Description <br /> |-<br /> |short<br /> |6<br /> |28<br /> |128 GB<br /> |00:05:00<br /> |Short queue with 5 minute time limit<br /> |-<br /> |normal<br /> |4<br /> |28<br /> |128 GB<br /> |08:00:00<br /> |Medium queue with 8 hour time limit<br /> |-<br /> |long<br /> |1<br /> |28<br /> |128 GB<br /> |168:00:00<br /> |Long queue with one week time limit<br /> |-<br /> |bigmem<br /> |1<br /> |24<br /> |750 GB<br /> |72:00:00<br /> |High memory queue with 3 day time limit<br /> |-<br /> |#mpi<br /> |1<br /> |112<br /> |128 GB<br /> |72:00:00<br /> |Queue for mpi parallel jobs with 3 day time limit<br /> |}<br /> <br /> # If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.<br /> <br /> === Additional information ===<br /> <br /> * A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].<br /> * Detailed reference documentation for queue submission is available [http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm here].</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-05-07T10:54:58Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 1,500 per year (to be confirmed soon).<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://storageadmin.bi.up.ac.za http://storageadmin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > lfs quota -u username /nlustre<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** 5 TB total (add 4)<br /> ** 10 TB<br /> ** 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2018-05-07T09:46:18Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=Wonko&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]<br /> * The Bioinformatics post-graduate lecture [https://docs.google.com/spreadsheets/d/1cPluvAnTzm9Wx-RFeisVo_OPFDMWoXWFdmySA4wEitg/edit?usp=sharing schedule] is available for any interested students from other departments to attend. Lectures are on Tuesdays and Thursdays at 10:00 in FABI Square 3-26</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-05-03T17:54:30Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 1,500 per year (to be confirmed soon).<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://trin.bi.up.ac.za http://trin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> > To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > lfs quota -u username /nlustre<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** Add 5 TB<br /> ** Add 10 TB<br /> ** Add 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-05-03T17:53:49Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 1,500 per year (to be confirmed soon).<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://trin.bi.up.ac.za http://trin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> > To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > lfs quota -u username<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** Add 5 TB<br /> ** Add 10 TB<br /> ** Add 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Storage_Quotas_and_Charges Storage Quotas and Charges 2018-05-03T17:53:30Z

<p>Fourie: </p> <hr /> <div>=== Pricing ===<br /> <br /> The price of a basic account is R 1,500 per year (to be confirmed soon).<br /> <br /> <br /> === Checking storage quotas ===<br /> <br /> * A web-based system for checking the different user and group storage quotas and charges is available at [http://trin.bi.up.ac.za http://trin.bi.up.ac.za].<br /> * Home directory quotas can be checked with:<br /> <source lang="c"><br /> > To be confirmed<br /> </source><br /> * nLustre quotas can be checked with:<br /> <source lang="c"><br /> > xxx<br /> </source><br /> <br /> <br /> === Storage ===<br /> <br /> A basic account provides:<br /> <br /> * 512 GB of storage space in /home/''user''<br /> * 1 TB of storage space in /nlustre/''user'' and /nlustre/scratch/''user''<br /> * 512 GB of storage space in Galaxy<br /> * Unlimited computational usage<br /> <br /> <br /> === Upgrading storage space ===<br /> * Storage space may be upgraded at R 1,000 per TB per year in the following steps:<br /> ** Add 5 TB<br /> ** Add 10 TB<br /> ** Add 20 TB or more</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:51:12Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://www.globus.org/app/transfer Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * The transfer will run in the background in using an optimized threaded transfer method<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:49:45Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://www.globus.org/app/transfer Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|1000px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:49:06Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://www.globus.org/app/transfer Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|800px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:48:49Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://www.globus.org/app/transfer Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * An example is shown below:<br /> [[File:globusexample.png|500px]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/File:Globusexample.png File:Globusexample.png 2018-05-03T17:47:26Z

<p>Fourie: Globus Transfer Example</p> <hr /> <div>Globus Transfer Example</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:46:28Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://www.globus.org/app/transfer Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> [[File:globusexample.png]]<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:44:39Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]<br /> * Log in at the [https://www.globus.org/app/transfer Globus Transfer site]<br /> * You will see two sections: one for each institution<br /> * One the left, for the UP bioinformatics Globus Connect server, type fourie#globusconnect at the endpoint link (this is not your login name, it is an endpoint definition that we have created for our UP bioinformatics server)<br /> * You will be prompted for your login name and password on the UP bioinformatics server, and will be able to see your files at UP once you have logged in. You can also change the directory to eg. /nlustre/users/username<br /> * On the right, provide the endpoint for the other institution's Globus endpoint. An example for the CHPC would be CHPC-Globus<br /> * You will be prompted for your login name and password on the other institutions's server, and will be able to see your files once you have logged in<br /> * You can now perform transfers of files or directories by selecting the item to transfer, and clicking on the arrow key in the relevant direction<br /> * Once your transfer has been initiated, you may leave the site, and will be notified by e-mail when the transfer has been completed</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:26:47Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [https://www.globusid.org/create Globus Connect Site Signup site]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:25:48Z

<p>Fourie: </p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at the [Globus Connect Site]</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Transferring_large_quantities_of_data_between_institutions Transferring large quantities of data between institutions 2018-05-03T17:24:52Z

<p>Fourie: Created page with "To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based in..."</p> <hr /> <div>To transfer large amounts of data between institutions, Globus Connect is the application of choice if supported by both institutions. It is designed to provide a web-based interface where you log in to the servers at both institutions, and perform a large threaded data transfer in the background.<br /> <br /> * Create a Globus Connect login at:</div>

Fourie http://wiki.bi.up.ac.za/wiki/index.php/Main_Page Main Page 2018-05-03T17:22:35Z

<p>Fourie: </p> <hr /> <div><strong>Welcome to the Centre for Bioinformatics and Computational Biology!</strong><br /> <br /> == Getting started ==<br /> * [[Obtaining an account]]<br /> * [[Logging in to a terminal session]]<br /> * [[Running jobs on our servers]]<br /> * [[Using the PBS / Torque queueing environment]]<br /> * [[Software resources]]<br /> * [[Hardware resources]]<br /> * [http://wiki.bi.up.ac.za/wiki/index.php?title=Storage_Quotas_and_Charges&action=edit&redlink=1 Storage Quotas and Charges]<br /> * [[Transferring large quantities of data between institutions]]<br /> * [[Backups]]<br /> * The compute infrastructure load can be seen in the [http://wonko.bi.up.ac.za/ganglia/?c=Wonko&m=load_one&r=hour&s=by%20name&hc=4&mc=2 ganglia monitor]</div>

Fourie