Mercurial > repos > malex > gaussian
changeset 1:28ebcfcb10a2 draft
Deleted to remove the extra folder level.
| author | malex |
|---|---|
| date | Tue, 18 Sep 2012 23:01:57 -0400 |
| parents | 33301cfd5fb1 |
| children | ed472dc06c20 |
| files | gaussian/gaussian.py gaussian/gaussian.xml gaussian/gaussian_datatype.xml gaussian/gaussian_job_rules.py |
| diffstat | 4 files changed, 0 insertions(+), 161 deletions(-) [+] |
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--- a/gaussian/gaussian.py Tue Sep 18 23:00:40 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -#/usr/bin/env python -""" -Copyright (C) 2012 -Ying Zhang <zhang@hpc.ufl.edu> and Oleksandr Moskalenko <om@hpc.ufl.edu> -University of Florida Research Computing - -This script checks the user permission for using gaussian software. -If permission is granted, it runs g09 with inputfile. - -It takes 2 command line options: - $name: the $__user_name__ template preset that corresponds to the real -username. - $inputfile: a input file for g09 -""" -import sys, os, shutil -from subprocess import Popen, PIPE - -if len(sys.argv) == 3: - name = sys.argv[1] - ginput = sys.argv[2] -else: - msg = "Error: wrong number of parameters provided.\n" - sys.stderr.write(msg) - sys.exit(1) - -command = "groups " + name + " | grep gaussian" -result = Popen([command], shell=True, stdout=PIPE, stderr=PIPE, close_fds=True) -stdout, stderr = result.communicate() -return_code = result.returncode -if return_code: - errmsg = "Error: only users in the gaussian group can use this software.\n" - sys.stdout.write(stdout) - sys.stderr.write(errmsg) - sys.stderr.write(stderr) - sys.stderr.write("Return error code %i from command:\n" % return_code) - sys.stderr.write("%s\n" % command) - sys.exit(2) -else: - if not os.path.exists('gaussian.com'): - shutil.copyfile(ginput, 'gaussian.com') - cmd = 'source /galaxy/run/dev/tools/chemistry/env.sh; g09 gaussian.com' - result = Popen([cmd], shell=True, stdout=PIPE, stderr=PIPE, close_fds=True) - stdout, stderr = result.communicate() - return_code = result.returncode - if return_code: - sys.stdout.write(stdout) - sys.stderr.write(stderr) - sys.stderr.write("Return error code %i from command:\n" % return_code) - sys.stderr.write("%s\n" % result) - sys.exit(1) - else: - sys.stdout.write(stdout) - sys.stdout.write(stderr) - sys.exit(0)
--- a/gaussian/gaussian.xml Tue Sep 18 23:00:40 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -<tool id="gaussian" name="Gaussian" version="1.0.0"> -<!-- -Copyright (C) 2012 -Ying Zhang <zhang@hpc.ufl.edu> and Oleksandr Moskalenko <om@hpc.ufl.edu> -University of Florida Research Computing ---> - <description>Computational Chemistry software for electronic structure modeling.</description> - <command interpreter="python">gaussian.py $__user_name__ $infile</command> - <inputs> - <param format="txt" name="infile" type="data" label="Gaussian Input File"/> - </inputs> - <outputs> - <data format="txt" name="outfile" type="data" from_work_dir="gaussian.log" label="${tool.name} on ${on_string}: Output" /> - </outputs> - <!-- - <stdio> - <exit_code range="1:" level="fatal" description="Tool Error - see debug log." /> - <exit_code range="2:" level="fatal" description="Unauthorized user - see help." /> - </stdio> - --> - <tests> - <test> - <param name="infile" value="chemistry/gaussian/gaussian.com"/> - <output name="outfile" file="chemistry/gaussian/gaussian.log"/> - </test> -</tests> - - <help> -**Gaussian version g09** - -Gaussian is Electronic Structure Modeling Software. It has license restrictions. -To run it you must sign the Gaussian Confidentiality Agreement. The agreement -form is available in NPB 2238 during normal business hours. - - -Running Gaussian from Galaxy is currently in testing stage. Please report any -problems to the `UF HPC Support <http://support.hpc.ufl.edu>`_. - - -Batch job resource request can be specified at the beginning of the input file -as in the following example: - -%nproc=8 - number of cores (ppn). - -%mem=2000mb - memory size (pmem) can be set in kb, mb, gb, kw, mw, or gw. Words are used as the default. - -!walltime=12:00:00 - run time (walltime) in HH:MM:SS format. - - -Detailed information on program usage is available from `the Gaussian website <http://www.gaussian.com/>`_. - </help> -</tool>
--- a/gaussian/gaussian_datatype.xml Tue Sep 18 23:00:40 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -<datatype extension="com" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="true"/>
--- a/gaussian/gaussian_job_rules.py Tue Sep 18 23:00:40 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,54 +0,0 @@ -def gaussian(job): - inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) - inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) - src_comfile = inp_data[ "infile" ].file_name - comfile = open(src_comfile, 'r') - ppn='1' - pmem = '900mb' - overhead = 200 - walltime = '11:59:59' - for line in comfile: - line = line.strip().lower() - if ( "%nproc=" in line): - try: - ppn = line.split('=')[1] - except Exception, e: - log.debug(e) - sys.stdout.write(e) - if ("%mem=" in line): - try: - mem_str = line.split('=')[1] - if ( "kb" in mem_str ): - mem_num = mem_str.split('kb')[0] - mem_num = int(int(mem_num) / 1024.0) + overhead - if ( "mb" in mem_str ): - mem_num = mem_str.split('mb')[0] - mem_num = int(mem_num) + overhead - elif ( "gb" in mem_str ): - mem_num = mem_str.split('gb')[0] - mem_num = (int(mem_num) * 1024) + overhead - elif ( "kw" in mem_str ): - mem_num = mem_str.split('kw')[0] - mem_num = int(int(mem_num) * 8 / 1024.0) + overhead - elif ( "mw" in mem_str ): - mem_num = mem_str.split('mw')[0] - mem_num = (int(mem_num) * 8) + overhead - elif ( "gw" in mem_str ): - mem_num = mem_str.split('gw')[0] - mem_num = (int(mem_num) * 8 * 1024) + overhead - else: - #Assume words - mem_num = int(int(mem_str) * 8 / 1024.0 / 1024.0) + overhead - pmem_num = int(mem_num / int(ppn)) - pmem = str(pmem_num) + 'mb' - except Exception, e: - log.debug(e) - sys.stdout.write(e) - if ("!walltime=" in line): - try: - walltime = line.split('=')[1] - except Exception, e: - log.debug(e) - sys.stdout.write(e) - request = "-l nodes=1:ppn=%s,pmem=%s,walltime=%s" % (ppn, pmem, walltime) - return 'drmaa://%s/' % request