Cluster Documentation - Revision history

Admin: /* Python */

2025-07-14T13:31:17Z

Python

← Older revision		Revision as of 15:31, 14 July 2025
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	3.10.16 64-bit call set python_310_64.bat		3.10.16 64-bit call set python_310_64.bat
	3.11.11 64-bit call set_python_311_64.bat		3.11.11 64-bit call set_python_311_64.bat
	3.12.8 64-bit call set_python_312_64.bat		3.12.11 64-bit call set_python_312_64.bat
	3.13.2 64-bit call set_python_313_64.bat		3.13.5 64-bit call set_python_313_64.bat

	</pre>		</pre>

Admin: /* Python */

2025-03-06T22:00:19Z

Python

← Older revision		Revision as of 00:00, 7 March 2025
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	3.11.11 64-bit call set_python_311_64.bat		3.11.11 64-bit call set_python_311_64.bat
	3.12.8 64-bit call set_python_312_64.bat		3.12.8 64-bit call set_python_312_64.bat
	3.13.1 64-bit call set_python_313_64.bat		3.13.2 64-bit call set_python_313_64.bat

	</pre>		</pre>

Admin: /* Python */

2025-01-20T21:33:00Z

Python

← Older revision		Revision as of 23:33, 20 January 2025
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	<pre>		<pre>
	2.7.18 64-bit call set_python_27_64.bat		2.7.18 64-bit call set_python_27_64.bat
	3.5.9 64-bit call set_python_35_64.bat		3.5.10 64-bit call set_python_35_64.bat
	3.6.15 64-bit call set python_36_64.bat		3.6.15 64-bit call set python_36_64.bat
	3.7.17 64-bit call set_python_37_64.bat		3.7.17 64-bit call set_python_37_64.bat
	3.8.17 64-bit call set python_38_64.bat		3.8.20 64-bit call set python_38_64.bat
	3.9.17 64-bit call set_python_39_64.bat		3.9.21 64-bit call set_python_39_64.bat
	3.10.12 64-bit call set python_310_64.bat		3.10.16 64-bit call set python_310_64.bat
	3.11.4 64-bit call ~~set_python_311_64~~.bat		3.11.11 64-bit call set_python_311_64.bat
			3.12.8 64-bit call set_python_312_64.bat
			3.13.1 64-bit call set_python_313_64.bat

	</pre>		</pre>

Admin at 16:58, 28 February 2024

2024-02-28T16:58:58Z

← Older revision		Revision as of 18:58, 28 February 2024
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	If you're using a machine that isn't actually logged into DIDE, then the client software will have a problem working out who you are. In this case, there are two things you need to do.		If you're using a machine that isn't actually logged into DIDE, then the client software will have a problem working out who you are. In this case, there are two things you need to do.
	* Check you've really got a DIDE username. If you don't know what it is, talk to your lovely IT team.		* Check you've really got a DIDE username. If you don't know what it is, talk to your lovely IT team.
	* Connect to the DIDE VPN ~~(see http://www1.imperial.ac.uk/publichealth/departments/ide/it/remote/) - login to that with your DIDE account.~~		* Connect to the DIDE VPN using ZScaler from https://uafiles.cc.ic.ac.uk/, and login to that with your IC account - but you'll still need your DIDE account to access DIDE servers after the ZScaler connection is up and running.
	* Alternatively to the DIDE VPN, you can install ICT's ZScaler from https://uafiles.cc.ic.ac.uk/, and login to that with your IC account - but you'll still need your DIDE account to access DIDE servers after the ZScaler connection is up and running.
	* Now we'll open a command window using "runas" - which lets you choose which identity the system thinks you are within that command window:-		* Now we'll open a command window using "runas" - which lets you choose which identity the system thinks you are within that command window:-
	<pre>		<pre>

Admin at 16:58, 28 February 2024

2024-02-28T16:58:09Z

← Older revision		Revision as of 18:58, 28 February 2024
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	* Check you've really got a DIDE username. If you don't know what it is, talk to your lovely IT team.		* Check you've really got a DIDE username. If you don't know what it is, talk to your lovely IT team.
	* Connect to the DIDE VPN (see http://www1.imperial.ac.uk/publichealth/departments/ide/it/remote/) - login to that with your DIDE account.		* Connect to the DIDE VPN (see http://www1.imperial.ac.uk/publichealth/departments/ide/it/remote/) - login to that with your DIDE account.
	* Alternatively to the DIDE VPN, you can install ICT's ~~Juniper client~~ from ~~http~~://~~secureaccess~~.~~imperial~~.ac.uk, and login to that with your IC account - but you'll still need your DIDE account to access DIDE servers after the ~~Juniper~~ connection is up and running.		* Alternatively to the DIDE VPN, you can install ICT's ZScaler from https://uafiles.cc.ic.ac.uk/, and login to that with your IC account - but you'll still need your DIDE account to access DIDE servers after the ZScaler connection is up and running.
	* Now we'll open a command window using "runas" - which lets you choose which identity the system thinks you are within that command window:-		* Now we'll open a command window using "runas" - which lets you choose which identity the system thinks you are within that command window:-
	<pre>		<pre>

Admin: /* Python */

2023-08-24T07:20:18Z

Python

← Older revision		Revision as of 09:20, 24 August 2023
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	=== Python ===		=== Python ===

	* ~~Many Python versions are available~~ on the cluster. Different python versions within the same release (e.g., 3.5.1 and 3.5.2) do not behave nicely together in automated installation, so if you have a desperate need for a previous minor version, get in touch. While 2.7.18 is available, we '''strongly''' recommend migrating away from Python 2.7, as it has been officially discontinued on 1st January 2020. Experiences may vary, and future success is not guaranteed.		* The most recent version of each major release is on the cluster. Different python versions within the same release (e.g., 3.5.1 and 3.5.2) do not behave nicely together in automated installation, so if you have a desperate need for a previous minor version, get in touch. While 2.7.18 is available, we '''strongly''' recommend migrating away from Python 2.7, as it has been officially discontinued on 1st January 2020. Experiences may vary, and future success is not guaranteed.

	<pre>		<pre>

Admin: /* Python */

2023-08-24T06:50:51Z

Python

← Older revision		Revision as of 08:50, 24 August 2023
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	=== Python ===		=== Python ===

	* ~~Current~~ Python versions available on the cluster ~~are 3.5, 3.6 and 3.7 based~~. Different python versions within the same release (e.g., 3.5.1 and 3.5.2) do not behave nicely together in automated installation, so if you have a desperate need for a previous minor version, get in touch. While 2.7.17 is available, we '''strongly''' recommend migrating away from Python 2.7, as it has been officially discontinued on 1st January 2020. Experiences may vary, and future success is not guaranteed~~. You have been warned..~~.		* Many Python versions are available on the cluster. Different python versions within the same release (e.g., 3.5.1 and 3.5.2) do not behave nicely together in automated installation, so if you have a desperate need for a previous minor version, get in touch. While 2.7.18 is available, we '''strongly''' recommend migrating away from Python 2.7, as it has been officially discontinued on 1st January 2020. Experiences may vary, and future success is not guaranteed.

	<pre>		<pre>
	2.7.17 64-bit call set_python_27_64.bat		2.7.18 64-bit call set_python_27_64.bat
	3.5.4 64-bit call set_python_35_64.bat		3.5.9 64-bit call set_python_35_64.bat
	3.6.8 64-bit call set python_36_64.bat		3.6.15 64-bit call set python_36_64.bat
	3.7.5 64-bit call set_python_37_64.bat</pre>		3.7.17 64-bit call set_python_37_64.bat
			3.8.17 64-bit call set python_38_64.bat
			3.9.17 64-bit call set_python_39_64.bat
			3.10.12 64-bit call set python_310_64.bat
			3.11.4 64-bit call set_python_311_64.bat

			</pre>

	* You'll most likely want to use some packages, so you'll need to have a network-accessible location to put your packages in. If you're running a version of Windows with Python that matches one installed on the cluster, then you'll be able to share that package repository between the two. But if you're running a different version, or a different operating system, or a different Python version, then you'll need to keep your local package repository separate from the one the cluster uses.		* You'll most likely want to use some packages, so you'll need to have a network-accessible location to put your packages in. If you're running a version of Windows with Python that matches one installed on the cluster, then you'll be able to share that package repository between the two. But if you're running a different version, or a different operating system, or a different Python version, then you'll need to keep your local package repository separate from the one the cluster uses.

Admin: /* Information for running any job */

2022-10-12T14:09:41Z

Information for running any job

← Older revision		Revision as of 16:09, 12 October 2022
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	Any executable/batch file that the cluster will run must be somewhere on the network that the cluster has access to, when it logs in as you. This amounts to any network accessible drive that you have access to when you login – including network shares, such as the temp drive, your home directory, and any specific network space set up for your project.		Any executable/batch file that the cluster will run must be somewhere on the network that the cluster has access to, when it logs in as you. This amounts to any network accessible drive that you have access to when you login – including network shares, such as the temp drive, your home directory, and any specific network space set up for your project.

	After a job is launched, all paths are relative to the `/workdir:` specified on the job submit command-line. Windows does not usually allow a network path to be the current directory, and MS-HPC somehow gets around this. But if in doubt, use fully-qualified paths to specify where files should be read from, or written to. You may want to write code that takes the paths from a parameter file, or as a command-line parameter, to give as much flexibility as possible.		After a job is launched, all paths are relative to the '''/workdir:''' specified on the job submit command-line. Windows does not usually allow a network path to be the current directory, and MS-HPC somehow gets around this. But if in doubt, use fully-qualified paths to specify where files should be read from, or written to. You may want to write code that takes the paths from a parameter file, or as a command-line parameter, to give as much flexibility as possible.

	Your home directory, and the temp drive are on departmental servers that don't have an especially fast connection to the cluster. So avoid having thousands of jobs all reading/writing to those places at once. Additionally, the temp drive is shared between all users, and your home drive has a limited quota. It is also backed up every day, so avoid using it as scratch storage for results you don’t actually want to keep. Generally, the shares you'll want to use from the clusters will be ones containing the word "NAS", which the big cluster has fast access to.		Your home directory, and the temp drive are on departmental servers that don't have an especially fast connection to the cluster. So avoid having thousands of jobs all reading/writing to those places at once. Additionally, the temp drive is shared between all users, and your home drive has a limited quota. It is also backed up every day, so avoid using it as scratch storage for results you don’t actually want to keep. Generally, the shares you'll want to use from the clusters will be ones containing the word "NAS", which the big cluster has fast access to.

Admin: /* Visibility */

2022-10-12T14:08:46Z

Visibility

← Older revision		Revision as of 16:08, 12 October 2022
Line 112:		Line 112:
	=== Visibility ===		=== Visibility ===

	~~First rule: the~~ executable ~~(or~~ batch) file that the cluster will run must be somewhere on the network that the cluster has access to, when it logs in as you. This amounts to any network accessible drive that you have access to when you login – including network shares, such as the temp drive, your home directory, and any specific network space set up for your project.		Any executable/batch file that the cluster will run must be somewhere on the network that the cluster has access to, when it logs in as you. This amounts to any network accessible drive that you have access to when you login – including network shares, such as the temp drive, your home directory, and any specific network space set up for your project.

	Do not ~~assume that~~ the ~~program will run in any specific~~ directory ~~– even though there are ways that are meant to do that~~. ~~Use full~~ paths to specify where files should be read from, or written to. You may want to write code that takes the paths ~~either~~ from a parameter file, or as a command-line parameter, to give as much flexibility as possible. ~~In the long run, this will help you more.~~		After a job is launched, all paths are relative to the `/workdir:` specified on the job submit command-line. Windows does not usually allow a network path to be the current directory, and MS-HPC somehow gets around this. But if in doubt, use fully-qualified paths to specify where files should be read from, or written to. You may want to write code that takes the paths from a parameter file, or as a command-line parameter, to give as much flexibility as possible.
	REMEMBER THAT your home directory is backed up every day – and it’s not generally very big. So please avoid filling it with enormous sets of results that you don’t actually want to keep – it will make lots of people happy if you can rather write your files to somewhere that doesn’t get backed up. Even a network share on your desktop will do…

	~~If you would like to create a network share on your desktop, then simply…~~		Your home directory, and the temp drive are on departmental servers that don't have an especially fast connection to the cluster. So avoid having thousands of jobs all reading/writing to those places at once. Additionally, the temp drive is shared between all users, and your home drive has a limited quota. It is also backed up every day, so avoid using it as scratch storage for results you don’t actually want to keep. Generally, the shares you'll want to use from the clusters will be ones containing the word "NAS", which the big cluster has fast access to.
	~~Right Click on the folder you’d like to share~~, and ~~choose “Share”~~
	~~The next page shows who has rights to~~ the ~~folder – by default, you!~~
	~~Click~~ on ~~Share.~~
	~~A share is created called \\your-computer-name\the-share-name~~
	~~And you’ll be able~~ to ~~access this from~~ the cluster.

	~~BUT~~, ~~there are limits on how many connections can be made to~~ your ~~desktop~~, so ~~a desktop share may be useful for testing, but not~~ for ~~running lots of jobs.~~

	If you ~~really need~~ to ~~map a network drive letter~~, ~~then at~~ the ~~top of your “run.bat” file:-~~
	~~net~~ use ~~X: \\your-computer-name\~~the~~-share-name~~

	~~Summary Comment: Try and use a project share on one of~~ the ~~proper servers~~.

	=== Interactivity ===		=== Interactivity ===

Admin: /* BOW (BioInformatics on Windows) */

2022-07-26T11:23:32Z

BOW (BioInformatics on Windows)

← Older revision		Revision as of 13:23, 26 July 2022
Line 503:		Line 503:
	\|-		\|-
	\| raxml		\| raxml
	\| 8.2.12 (~~pthreads~~)		\| 8.2.12 (best for each node)
	\|-		\|-
	\| raxml_sse3		\| raxml_sse3
Line 510:		Line 510:
	\| raxml_avx		\| raxml_avx
	\| 8.2.12 (pthreads+avx)		\| 8.2.12 (pthreads+avx)
			\|-
			\| raxml_avx2
			\| 8.2.12 (pthreads+avx2)
	\|}		\|}

	Note that BWA-MEM is hardwired to use a linux-only feature, so will produce an odd message and not do what you want if you use that mode on Windows. However, it seems that minimap2 may be a faster and more accurate way		Note that BWA-MEM is hardwired to use a linux-only feature, so will produce an odd message and not do what you want if you use that mode on Windows. However, it seems that minimap2 may be a faster and more accurate way
	of doing what bwa does in any case, and that seems to have no such limitation.		of doing what bwa does in any case, and that seems to have no such limitation.

			Also, note that raxml.exe is a copy of the most optimised build for the particular cluster node the job is running on. fi--dideclusthn only supports SSE3;
			fi--didemrchnb varies a little; the 32-cores support AVX2, the 24, 20 and 16 core machines support AVX, and only the oldest 12-core nodes only support SSE3. You don't have to worry about, except to expect performance to vary between them.

	=== GATK and Picard ===		=== GATK and Picard ===