Skip to content

Instantly share code, notes, and snippets.

View pescobar's full-sized avatar

Pablo Escobar Lopez pescobar

60 followers · 28 following
  • UniBas - SIB
View GitHub Profile
@pescobar
pescobar / fix
Created February 20, 2013 14:33
host2avail_mem = {}
host2avail_slots = {}
for h in hosts:
hinfo = commands.getoutput("qconf -se %s" %h)
if re.search(H_VMEMMATCH_m, hinfo):
mem_match = re.search(H_VMEMMATCH_m, hinfo)
else:
print 'not found h_vmem consumable resource in ' + h
sys.exit()
if re.search("[\s,]?slots=(\d+)", hinfo, re.MULTILINE):
@pescobar
pescobar / gist:5003865
Created February 21, 2013 10:46
#!/usr/bin/env python
import commands
from string import strip
#def get_hosts_for_user(user):
#hosts = map(strip, commands.getoutput('qstat -s r -u ' + user + ' | grep -v job-ID |grep -v\
#\'\-\-\'|awk {\'print $8\'}|awk -F \"@\" {\'print $2\'} |awk -F \'.\'\
#{\'print $1\'}').split("\n"))
@pescobar
pescobar / gist:5311968
Last active December 15, 2015 19:29
sge jsv for java jobs memory reservation
#!/bin/bash
jsv_on_start() {
return
}
jsv_on_verify() {
# for debugging
#params=$(jsv_show_params)
#jsv_log_info "$params"
@pescobar
pescobar / gist:7546200
Created November 19, 2013 14:31
eb debug log
[pub@login11 cap3]$ cat /scratch/easybuild-C0UyT4.log
== 2013-11-19 15:27:48,758 main INFO This is EasyBuild 1.9.0 (framework: 1.9.0, easyblocks: 1.9.0) on host login11.
== 2013-11-19 15:27:48,758 main.filetools DEBUG run_cmd: running cmd which eb (in /tmp/cap3)
== 2013-11-19 15:27:48,766 main.filetools DEBUG cmd "which eb" exited with exitcode 0 and output:
/import/bc2/soft/centos6/software/EasyBuild/1.9.0/bin/eb
== 2013-11-19 15:27:48,767 main.filetools DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)
== 2013-11-19 15:27:48,767 main.easyconfig.tools DEBUG Also considering installation prefix /import/bc2/soft/centos6/software/EasyBuild/1.9.0...
== 2013-11-19 15:27:48,768 main.easyconfig.tools DEBUG Looking for easybuild/easyconfigs in path /import/bc2/soft/centos6/software/EasyBuild/1.9.0/lib/python2.6/site-packages/easybuild_framework-1.9.0-py2.6.egg/easybuild/easybuild/easyconfigs
== 2013-11-19 15:27:48,768 main.easyconfig.tools DEBUG Looking for easy
@pescobar
pescobar / gist:7683025
Created November 27, 2013 20:54
eb log
This file has been truncated, but you can view the full file.
== 2013-11-27 17:23:23,866 main.ConfigureMake INFO This is EasyBuild 1.9.0 (framework: 1.9.0, easyblocks: 1.9.0) on host login11.
== 2013-11-27 17:23:23,866 main.ConfigureMake INFO Init completed for application name o2scl version 0.913
== 2013-11-27 17:23:23,866 main INFO Obtained application instance of for o2scl (easyblock: None)
== 2013-11-27 17:23:23,867 main.ConfigureMake INFO building and installing o2scl/0.913...
== 2013-11-27 17:23:23,868 main.ConfigureMake INFO fetching files...
== 2013-11-27 17:23:23,868 main.ConfigureMake INFO Starting fetch step
== 2013-11-27 17:23:23,870 main.ConfigureMake INFO Running method fetch_step part of step fetch
== 2013-11-27 17:23:23,870 main.ConfigureMake WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2013-11-27 17:23:23,879 main.ConfigureMake INFO Found file o2scl-0.913.tar.gz at /tmp/easybuild-test/source/o/o2scl/o2scl-0.913.tar.gz
== 2013-11-27 17:23:23,880 main.ConfigureMake INFO Added sources: [
@pescobar
pescobar / debug log
Created November 27, 2013 21:10
This file has been truncated, but you can view the full file.
[pub@login11 ~]$ cat /scratch/easybuild-D7WO2F.log
== 2013-11-27 22:04:10,004 main INFO This is EasyBuild 1.9.0 (framework: 1.9.0, easyblocks: 1.9.0) on host login11.
== 2013-11-27 22:04:10,005 main.filetools DEBUG run_cmd: running cmd which eb (in /import/bc2/home/admin/pub)
== 2013-11-27 22:04:10,013 main.filetools DEBUG cmd "which eb" exited with exitcode 0 and output:
/import/bc2/soft/centos6/software/EasyBuild/1.9.0/bin/eb
== 2013-11-27 22:04:10,013 main.filetools DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)
== 2013-11-27 22:04:10,014 main.easyconfig.tools DEBUG Also considering installation prefix /import/bc2/soft/centos6/software/EasyBuild/1.9.0...
== 2013-11-27 22:04:10,014 main.easyconfig.tools DEBUG Looking for easybuild/easyconfigs in path /import/bc2/soft/centos6/software/EasyBuild/1.9.0/lib/python2.6/site-packages/easybuild_framework-1.9.0-py2.6.egg/easybuild/easybuild/easyconfigs
== 2013-11-27 22:04:10,015 main.easyconfig.tools DEBUG Lo
@pescobar
pescobar / gist:7918438
Created December 11, 2013 21:05
== 2013-12-11 22:01:02,339 main.environment INFO Environment variable PATH set to /import/bc2/soft/centos6/software/EasyBuild/1.9.0/bin:/import/bc2/soft/system/UGE/current/bin/lx-amd64:/import/bc2/home/admin/pub/pub/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:.:/import/bc2/soft/centos6/software/lua/5.1.4.5/bin:/import/bc2/soft/centos6/software/lmod/lmod/libexec
== 2013-12-11 22:01:02,339 main.environment INFO Environment variable EBROOTEASYBUILD set to /import/bc2/soft/centos6/software/EasyBuild/1.9.0
== 2013-12-11 22:01:02,340 main.environment INFO Environment variable EBVERSIONEASYBUILD set to 1.9.0
== 2013-12-11 22:01:02,340 main.environment INFO Environment variable MODULEPATH set to /import/bc2/soft/centos6/modules/all:/import/bc2/soft/centos6/modules/base:/import/bc2/soft/centos6/modules/bio:/import/bc2/soft/centos6/modules/chem:/import/bc2/soft/centos6/modules/compiler:/import/bc2/soft/centos6/modules/data:/import/bc2/soft/centos6/modules/devel:/import/bc2/soft/centos6/modules/lang:/import/b
@pescobar
pescobar / gist:7918707
Created December 11, 2013 21:23
This file has been truncated, but you can view the full file.
== 2013-12-11 22:08:17,209 main INFO This is EasyBuild 1.9.0 (framework: 1.9.0, easyblocks: 1.9.0) on host login10.
== 2013-12-11 22:08:17,210 main.filetools DEBUG run_cmd: running cmd which eb (in /import/bc2/soft/centos6/installed_eb_files/Python)
== 2013-12-11 22:08:17,217 main.filetools DEBUG cmd "which eb" exited with exitcode 0 and output:
/import/bc2/soft/centos6/software/EasyBuild/1.9.0/bin/eb
== 2013-12-11 22:08:17,218 main.filetools DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w)
== 2013-12-11 22:08:17,219 main.easyconfig.tools DEBUG Also considering installation prefix /import/bc2/soft/centos6/software/EasyBuild/1.9.0...
== 2013-12-11 22:08:17,219 main.easyconfig.tools DEBUG Looking for easybuild/easyconfigs in path /import/bc2/soft/centos6/software/EasyBuild/1.9.0/lib/python2.6/site-packages/easybuild_framework-1.9.0-py2.6.egg/easybuild/easybuild/easyconfigs
== 2013-12-11 22:08:17,220 main.easyconfig.tools DEBUG Looking for easybuild/easycon
@pescobar
pescobar / gist:8323332
Created January 8, 2014 19:49
sickle with versionsuffix
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel
easyblock='MakeCp'
name = "sickle"
# version checked running "sickle --version"
version = "1.210"
@pescobar
pescobar / gist:8560808
Created January 22, 2014 15:33
argtable eb file
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
# Author: Pablo Escobar Lopez
# Swiss Institute of Bioinformatics
# Biozentrum - University of Basel
name = 'argtable'
version = '2.13'
homepage = 'http://argtable.sourceforge.net/'
description = """ Argtable is an ANSI C library for parsing GNU style