Molecular chemistry cluster - Revision history

Wtitulaer at 12:20, 28 June 2024

2024-06-28T12:20:46Z

← Older revision		Revision as of 12:20, 28 June 2024
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	The molecular chemistry cluster is comprised of cn100-103 and cn142 ~~(see [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Molecular software]])~~. Access to the cluster needs to be requested as detailed in [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Requesting access]].		The molecular chemistry cluster is comprised of cn100-103 and cn142. Access to the cluster needs to be requested as detailed in [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Requesting access]]. Currently we have the following running setup:

			{\| class="wikitable" style="margin:auto"
			\|+Cluster nodes of the Molecular Chemistry cluster
			\|-
			!Name of the node !! CPU !! RAM !! GPU !! Main group(s)
			\|-
			\| cn100 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn101 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn102 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn103 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn142 \|\| 2x 20-core Intel Xeon Silver 4416+ \|\| 256 GB \|\| 2x RTX A4000 \|\| molmech
			\|}



	== Logging in on cn142 ==		== Logging in on cn142 ==

Wtitulaer at 12:18, 28 June 2024

2024-06-28T12:18:37Z

← Older revision		Revision as of 12:18, 28 June 2024
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	Cn142 (like many Linux systems) has the following relevant directories which you should be aware of:		Cn142 (like many Linux systems) has the following relevant directories which you should be aware of:
	* '''/opt''' stores all optional software for the node. Most modelling software is actually found at /opt/molmech with soft-link executables in /opt/molmech/bin.		* '''/opt''' stores all optional software for the node. Most modelling software is actually found at /opt/molmech with soft-link executables in /opt/molmech/bin.
	* '''/scratch''' is meant for temporary data storage. When submitting computational jobs, this is where the system will most often ~~save~~ your ~~working~~ files. '''Keep in mind /scratch is for temporary storage and hence data can be purged without warning to the users '''.		* '''/scratch''' is meant for temporary data storage. When submitting computational jobs, this is where the system will most often read&write your files. At the end of the job you should move your output/input to a different directory to allow for enough space for other users. '''Keep in mind /scratch is for temporary storage and hence data can be purged without warning to the users '''.
	* '''/vol ''' which is unlike the others not a local directory but instead a directory shared between multiple nodes. /vol/nmrspectra/ for instance is the directory where you normally retrieve your recorded NMR-spectra from. Keep in mind however not all nodes import all /vol options (the SynOrgChem drive is for instance accessible from lilo but not from cn142).		* '''/vol ''' which is unlike the others not a local directory but instead a directory shared between multiple nodes. /vol/nmrspectra/ for instance is the directory where you normally retrieve your recorded NMR-spectra from. Keep in mind however not all nodes import all /vol options (the SynOrgChem drive is for instance accessible from lilo but not from cn142).
	'''/home/user/''' which is also not a local directory but is your science-account directory (replace user with your username). For instance /home/user/Desktop has the desktop files etc. you would see when you log in to a Huygens pc with your science-account. Keep in mind you have limited storage at this directory so use it wisely.		'''/home/user/''' which is also not a local directory but is your science-account directory (replace user with your username). For instance /home/user/Desktop has the desktop files etc. you would see when you log in to a Huygens pc with your science-account. Keep in mind you have limited storage at this directory so use it wisely.

Wtitulaer at 12:16, 28 June 2024

2024-06-28T12:16:58Z

← Older revision		Revision as of 12:16, 28 June 2024
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	'''/home/user/''' which is also not a local directory but is your science-account directory (replace user with your username). For instance /home/user/Desktop has the desktop files etc. you would see when you log in to a Huygens pc with your science-account. Keep in mind you have limited storage at this directory so use it wisely.		'''/home/user/''' which is also not a local directory but is your science-account directory (replace user with your username). For instance /home/user/Desktop has the desktop files etc. you would see when you log in to a Huygens pc with your science-account. Keep in mind you have limited storage at this directory so use it wisely.

	On cn142 we use SLURM for managing computational resources among so-called jobs: computational tasks. With a SLURM submission script for instance you can specify the amount of memory & CPU needed for your job and SLURM will then schedule your job and those of other users. For this ~~we have~~ the partition '''molmech'''. Should you wish to run larger jobs (for instance large-scale dockings with DOCK 3.8), you may need to submit the job to a different partition ~~(other~~		On cn142 we use SLURM for managing computational resources among so-called jobs: computational tasks. With a SLURM submission script for instance you can specify the amount of memory & CPU needed for your job and SLURM will then schedule your job and those of other users. For this purpose you submit a job to a partition: a sort of queue which specifies which nodes/computers the job can go to, who can submit jobs and if there are time or memory restrictions. In our case this is generally the partition ''molmech'' which will run the job on cn142. Should you wish to run larger jobs (for instance large-scale dockings with DOCK 3.8), you may need to submit the job to a different partition, which likely requires different permissions as well.

	~~The general intended workflow of using cn142 is:~~
	* Do a small-scale test run with the software you intend to use. ~~This step should be using minimal computing resources~~
	* Submit the computational task as a SLURM-s

			SLURM is very efficient at managing the resources of computing node(s) but it does not generally recognize commands running locally from users. For instance if you use python on cn142 locally, this is not communicated well to SLURM job scheduler. Hence, when you require multiple cores, a GPU or more than 8 GB RAM, you should ensure you submit your calculating task as a SLURM job. Depending on the software you are using, there are already pre-written examples of how to do this. Should you find this challenging, feel free to contact either wtitulaer or C&CZ.

	== Small guide for first time Linux users ==		== Small guide for first time Linux users ==
Line 27:		Line 24:
	sinfo		sinfo
	squeueu		squeueu
			sbatch
	kill		kill
	top u		top u
	module		module
	ln -s		ln -s

Wtitulaer at 12:11, 28 June 2024

2024-06-28T12:11:29Z

← Older revision		Revision as of 12:11, 28 June 2024
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	* '''/opt''' stores all optional software for the node. Most modelling software is actually found at /opt/molmech with soft-link executables in /opt/molmech/bin.		* '''/opt''' stores all optional software for the node. Most modelling software is actually found at /opt/molmech with soft-link executables in /opt/molmech/bin.
	* '''/scratch''' is meant for temporary data storage. When submitting computational jobs, this is where the system will most often save your working files. '''Keep in mind /scratch is for temporary storage and hence data can be purged without warning to the users '''.		* '''/scratch''' is meant for temporary data storage. When submitting computational jobs, this is where the system will most often save your working files. '''Keep in mind /scratch is for temporary storage and hence data can be purged without warning to the users '''.
	* '''/vol ''' which is unlike the others not a local dr		* '''/vol ''' which is unlike the others not a local directory but instead a directory shared between multiple nodes. /vol/nmrspectra/ for instance is the directory where you normally retrieve your recorded NMR-spectra from. Keep in mind however not all nodes import all /vol options (the SynOrgChem drive is for instance accessible from lilo but not from cn142).
			'''/home/user/''' which is also not a local directory but is your science-account directory (replace user with your username). For instance /home/user/Desktop has the desktop files etc. you would see when you log in to a Huygens pc with your science-account. Keep in mind you have limited storage at this directory so use it wisely.

	On cn142 we use SLURM for managing computational resources among so-called jobs: computational tasks. With a SLURM submission script for instance you can specify the amount of memory & CPU needed for your job and SLURM will then schedule your job and those of other users. For this we have the partition '''molmech'''. Should you wish to run larger jobs (for instance large-scale dockings with DOCK 3.8), you may need to submit the job to a different partition (other		On cn142 we use SLURM for managing computational resources among so-called jobs: computational tasks. With a SLURM submission script for instance you can specify the amount of memory & CPU needed for your job and SLURM will then schedule your job and those of other users. For this we have the partition '''molmech'''. Should you wish to run larger jobs (for instance large-scale dockings with DOCK 3.8), you may need to submit the job to a different partition (other
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	== Small guide for first time Linux users ==		== Small guide for first time Linux users ==
			I would recommend following this guide if this is your first-time using Linux: https://ubuntu.com/tutorials/command-line-for-beginners#1-overview (taken from the TheoChem wiki).
			But here follows a list of commands that may be useful which may not be in your usual tutorial (keep in mind this list may not be comprehensive):
			ncdu
			scontrol show node cn142
			sinfo
			squeueu
			kill
			top u
			module
			ln -s

Wtitulaer at 11:55, 28 June 2024

2024-06-28T11:55:48Z

← Older revision		Revision as of 11:55, 28 June 2024
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	== Logging in on cn142 ==		== Logging in on cn142 ==
	Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo with ~~{{Inline-code\|1=~~ssh user@lilo8.science.ru.nl}}		Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo with 'ssh user@lilo8.science.ru.nl' (described in https://cncz.science.ru.nl/nl/howto/ssh/). Afterwards you can log into cn142 by 'ssh cn142'.

			In order for the molecular modelling software to boot correctly, a set of environment variables etc. need to be set. This is achieved by 'source /opt/molmech/login_molmech.sh'. Afterwards programmes on cn142 (apart from Gaussian) should function as intended. Most programs also have their special set of settings which were compiled into modules. To see which modules are available use 'module avail'. Use 'module load X' to load module X and use 'module unload X' to unload it again. Additional options can be viewed with 'module --help'.

			== Cn142 directory structure ==
			Cn142 (like many Linux systems) has the following relevant directories which you should be aware of:
			* '''/opt''' stores all optional software for the node. Most modelling software is actually found at /opt/molmech with soft-link executables in /opt/molmech/bin.
			* '''/scratch''' is meant for temporary data storage. When submitting computational jobs, this is where the system will most often save your working files. '''Keep in mind /scratch is for temporary storage and hence data can be purged without warning to the users '''.
			* '''/vol ''' which is unlike the others not a local dr

			On cn142 we use SLURM for managing computational resources among so-called jobs: computational tasks. With a SLURM submission script for instance you can specify the amount of memory & CPU needed for your job and SLURM will then schedule your job and those of other users. For this we have the partition '''molmech'''. Should you wish to run larger jobs (for instance large-scale dockings with DOCK 3.8), you may need to submit the job to a different partition (other

			The general intended workflow of using cn142 is:
			* Do a small-scale test run with the software you intend to use. This step should be using minimal computing resources
			* Submit the computational task as a SLURM-s


			== Small guide for first time Linux users ==

Wtitulaer at 11:31, 28 June 2024

2024-06-28T11:31:32Z

← Older revision		Revision as of 11:31, 28 June 2024
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	== Logging in on cn142 ==		== Logging in on cn142 ==
	Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo ~~by:~~		Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo with {{Inline-code\|1=ssh user@lilo8.science.ru.nl}}

	{{code\|~~lang~~=~~css\|font-family: 'Times New Roman', serif;~~}}

Wtitulaer at 11:29, 28 June 2024

2024-06-28T11:29:53Z

← Older revision		Revision as of 11:29, 28 June 2024
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	Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:		Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:

	{{code\|lang=css\|font-family: 'Times New Roman', serif;}		{{code\|lang=css\|font-family: 'Times New Roman', serif;}}

Wtitulaer at 11:29, 28 June 2024

2024-06-28T11:29:45Z

← Older revision		Revision as of 11:29, 28 June 2024
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	Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:		Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:

	{{code\| ~~ssh user@lilo8.science.ru.nl}~~}		{{code\|lang=css\|font-family: 'Times New Roman', serif;}

Wtitulaer at 11:29, 28 June 2024

2024-06-28T11:29:11Z

← Older revision		Revision as of 11:29, 28 June 2024
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	== Logging in on cn142 ==		== Logging in on cn142 ==
	Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:		Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:
	{{code~~\|lang=bash~~\| ssh user@lilo8.science.ru.nl}}
			{{code\| ssh user@lilo8.science.ru.nl}}

Wtitulaer at 11:27, 28 June 2024

2024-06-28T11:27:53Z

← Older revision		Revision as of 11:27, 28 June 2024
Line 1:		Line 1:
	The molecular chemistry cluster is comprised of cn100-103 and cn142 (see [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Molecular software]]). Access to the cluster needs to be requested as detailed in [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Requesting access]]		The molecular chemistry cluster is comprised of cn100-103 and cn142 (see [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Molecular software]]). Access to the cluster needs to be requested as detailed in [[Molecular software#Applying for access to the Molecular Chemistry cluster\|Requesting access]].

			== Logging in on cn142 ==
			Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo by:
			{{code\|lang=bash\| ssh user@lilo8.science.ru.nl}}