NECI-testcode - Revision history

import>Js615: /* Setting up the testcode */

2010-07-14T15:11:25Z

Setting up the testcode

← Older revision		Revision as of 15:11, 14 July 2010
Line 12:		Line 12:
	anything created within the CLEAN directory inherits the group ownership of the		anything created within the CLEAN directory inherits the group ownership of the
	CLEAN directory rather than the default group of the user (which is normally a		CLEAN directory rather than the default group of the user (which is normally a
	group containing just that user). Please set umask 2 in your ~/.bashrc before		group containing just that user). Please set umask 0002 in your ~/.bashrc before
	changing files in the CLEAN directory so that the group retains write		changing files in the CLEAN directory so that the group retains write
	permissions on files modified by you within the CLEAN directory.		permissions on files modified by you within the CLEAN directory.
Line 181:		Line 181:

	PP_LIBRARY_PATH=/home/js615/CLEAN/CPMD/PP_LIBRARY		PP_LIBRARY_PATH=/home/js615/CLEAN/CPMD/PP_LIBRARY
	30 01 * * * umask 2 && /home/js615/CLEAN/testcode/main_testcode/tools/checktest.py		30 01 * * * umask 0002 && /home/js615/CLEAN/testcode/main_testcode/tools/checktest.py

	Re-stating the pseudopotential library path and umask 2 are required since cron		Re-stating the pseudopotential library path and umask 0002 are required since cron
	doesn't source your ~/.bashrc. The following line runs checktest.py with the		doesn't source your ~/.bashrc. The following line runs checktest.py with the
	default settings at 1.30am.		default settings at 1.30am.

import>Js615: /* Setting up the testcode */

2009-10-16T16:31:46Z

Setting up the testcode

← Older revision		Revision as of 16:31, 16 October 2009
Line 199:		Line 199:
	Though JSS has suggested:		Though JSS has suggested:

	#!/bin/bash		#!/bin/bash
		⚫	set_perms_on_dir=~/test

		⚫	chgrp -R alavi $set_perms_on_dir

	set_perms_on_dir~~=~/test~~		for file in $(find $set_perms_on_dir); do


⚫	~~chgrp~~ -R ~~alavi $~~set_perms_on_dir


⚫	~~for~~ ~~file~~ in ~~$(find~~ $set_perms_on_dir~~); do~~

	# Get user's permissions		# Get user's permissions

	perm=$(getfacl $file 2> /dev/null \| grep user \| sed -e 's/user:://')		perm=$(getfacl $file 2> /dev/null \| grep user \| sed -e 's/user:://')

	chmod g=$perm $file		chmod g=$perm $file

	if [ -d $file ]; then		if [ -d $file ]; then

	chmod g+s $file		chmod g+s $file

	fi		fi
		⚫	done

⚫	done

	==Other Users on scepter==		==Other Users on scepter==

import>Js615: /* Setting up the testcode */

2009-10-16T16:31:07Z

Setting up the testcode

← Older revision		Revision as of 16:31, 16 October 2009
Line 196:		Line 196:

	Then it will not have the correct permissions. The best way to fix this is to start again...		Then it will not have the correct permissions. The best way to fix this is to start again...

			Though JSS has suggested:

			#!/bin/bash


			set_perms_on_dir=~/test


			chgrp -R alavi $set_perms_on_dir


			for file in $(find $set_perms_on_dir); do

			# Get user's permissions

			perm=$(getfacl $file 2> /dev/null \| grep user \| sed -e 's/user:://')

			chmod g=$perm $file

			if [ -d $file ]; then

			chmod g+s $file

			fi

			done

	==Other Users on scepter==		==Other Users on scepter==

import>Js615 at 16:27, 16 October 2009

2009-10-16T16:27:31Z

← Older revision		Revision as of 16:27, 16 October 2009
Line 200:		Line 200:

	To use the test code on scepter, simply put umask 2 in your .bashrc, and then you can use testcode.py. If you want to use checktest.py, this will require re-compilation of the components, so will require you to have links to the libraries. You can either compile your own, or use mine. To use mine, simply copy my privatemodules folder (in /home/js615/) to your home directory. Then you should be able to use checktest.py.		To use the test code on scepter, simply put umask 2 in your .bashrc, and then you can use testcode.py. If you want to use checktest.py, this will require re-compilation of the components, so will require you to have links to the libraries. You can either compile your own, or use mine. To use mine, simply copy my privatemodules folder (in /home/js615/) to your home directory. Then you should be able to use checktest.py.

			==Setting up other testcodes==

			I've just set another testcode up with vasp (with group permissions) at:

			scepter:/home/js615/CLEANVASP

			The steps taken were:

			1. Made a clean directory and checked out code as above

			2. Added this block to the userconfig file:

			[vasp]
			exe = /home/js615/CLEANVASP/VASP/vasp
			cleanexe = /home/js615/CLEANVASP/VASP/vasp
			timing_output = cpu elapsed
			inp = INCAR
			repository_location = https://wwmm.ch.cam.ac.uk/svn2/groups/alavi/VASP/vasp.5/trunk
			compile = ./croncompile PLATFORM
			vcs = svn
			submit_template = /home/js615/CLEAN/testcode/main_testcode/tools/neci-submit.sh
			extract = /home/js615/CLEANVASP/testcode/main_testcode/tools/extractvasp.pl

			(not all of these features I'm using, but this is basically just a duplicate of the NECI block slightly altered).

			3. Then defined new jobs in jobconfig:

			[VASP_test]
			type = vasp

			# Form job categories.
			[categories]
			VASP = VASP_test

			4. Made a croncompile script, which is very simple since I'm only wanting to test VASP on ifort/mpi (so no dealing with PLATFORM variables, and no loading of modules)

			#!/bin/bash
			cp ump2_aG.F ump2.F
			cd ../NECI/
			make neci-vasp
			stat=$?
			if [ $stat -ne 0 ] ; then
			exit $stat
			fi
			cd ../VASP/
			make vasp

			5. Made a very simple data extraction script just for vasp DFT/HF output (more to be added)

			js615@scepter:~/CLEANVASP/testcode/main_testcode/tools> vi extractvasp.pl

			#!/usr/bin/perl -w
			$out=$ARGV[0];
			`cat OUTCAR >> $out`;
			$energy=`grep TOTEN $out \| head -1 \| tr -d "[:alpha:][:blank:]="`;
			print "energy\n";
			print "$energy";

			6. Made my test (VASP_test) and benchmarked it:

			js615@scepter:~/CLEANVASP/testcode> ./testcode.py --runbenchmark

			7. Added one platform block to the checktest_config file:

			[PC-ifort64-MPI]
			modules = ifort/64/11.0/074 mpi/openmpi/64/intel11/1.3.1
			options = --cores=1

			And modified the emailing.

			8. Ran checktest.py.

import>Js615: /* Setting up the testcode */

2009-10-16T13:13:05Z

Setting up the testcode

← Older revision		Revision as of 13:13, 16 October 2009
Line 79:		Line 79:

	See [[Lapack compilation]] for more information on compiling lapack.		See [[Lapack compilation]] for more information on compiling lapack.

			You'll also need python libraries.

	3. Setting up the libraries as modules		3. Setting up the libraries as modules

import>Jss43: /* Setting up the testcode */

2009-10-13T16:34:06Z

Setting up the testcode

@@ Line 193: / Line 193: @@
   chmod 2775 CLEAN
-Then it will not have the correct permissions.
+Then it will not have the correct permissions.  The best way to fix this is to start again...
 ==Other Users on scepter==

import>Jss43: /* Setting up the testcode */

2009-10-13T16:07:48Z

Setting up the testcode

← Older revision		Revision as of 16:07, 13 October 2009
Line 23:		Line 23:
	chmod 2775 CLEAN		chmod 2775 CLEAN
	cd CLEAN		cd CLEAN
⚫	svn co $SVN/~~NECI/trunk~~ ~~NECI~~
	svn co $SVN/CPMD/branches/QMC/trunk CPMD		svn co $SVN/CPMD/branches/QMC/trunk CPMD
	git clone scepter:~ajwt3/NECI.git NECI		git clone scepter:~ajwt3/NECI.git NECI
		⚫	svn co $SVN/testcode testcode

	Currently, svn and git are supported by the testcode.		Currently, svn and git are supported by the testcode.

import>Js615 at 15:34, 13 October 2009

2009-10-13T15:34:34Z

← Older revision		Revision as of 15:34, 13 October 2009
Line 209:		Line 209:
	fi		fi
	done		done

			==Other Users on scepter==

			To use the test code on scepter, simply put umask 2 in your .bashrc, and then you can use testcode.py. If you want to use checktest.py, this will require re-compilation of the components, so will require you to have links to the libraries. You can either compile your own, or use mine. To use mine, simply copy my privatemodules folder (in /home/js615/) to your home directory. Then you should be able to use checktest.py.

import>Js615: /* Setting up the testcode */

2009-10-13T15:20:24Z

Setting up the testcode

← Older revision		Revision as of 15:20, 13 October 2009
Line 200:		Line 200:
	for file in `find . -type f`; do		for file in `find . -type f`; do
	chmod 0000 $file		chmod 0000 $file
	~~chm d~~ ug=rw $file		chmod ug=rw $file
	i=`file $file \| grep script \| wc -l`		i=`file $file \| grep script \| wc -l`
	if [ $i = "1" ]; then		if [ $i = "1" ]; then

import>Js615: /* Setting up the testcode */

2009-10-13T15:13:07Z

Setting up the testcode

← Older revision		Revision as of 15:13, 13 October 2009
Line 186:		Line 186:

	6. Setting permissions		6. Setting permissions

			If the CLEAN directory isn't made with the statements in 1:

			mkdir CLEAN
			chgrp alavi CLEAN
			chmod 2775 CLEAN

			Then it will not have the correct permissions.

	There are two ways of getting the correct permissions, but the neater version written by JSS only works under certain non-default conditions (using ACLs, as are present on discovery).		There are two ways of getting the correct permissions, but the neater version written by JSS only works under certain non-default conditions (using ACLs, as are present on discovery).