Hi Vali, instead of using the bootstrap method I prefer to install easybuild like this:
$> wget https://raw.githubusercontent.com/hpcugent/easybuild-easyconfigs/master/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb $> git clone https://github.com/hpcugent/easybuild-easyconfigs.git $> git clone https://github.com/hpcugent/easybuild-easyblocks.git $> git clone https://github.com/hpcugent/easybuild-framework.git $> export PYTHONPATH="`pwd`/easybuild-framework:`pwd`/easybuild-easyblocks:`pwd`/easybuild-easyconfigs" $> export PATH=$PATH:`pwd`/easybuild-framework and then: $> eb --installpath=/soft --subdir-software=apps --subdir-modules=modules --sourcepath=/soft/sources --repositorypath=/soft/installed_easyconfigs EasyBuild-1.14.0.eb --try-software-version=1.15.2 that will install the latest release of easybuild (1.15.2) to /soft/apps and the easybuild module to /soft/modules. Then you just need to add /soft/modules/all to your $MODULEPATH , load the easybuild module and start using it. Of course you can adapt the paths to your preferred ones maybe you can give that approach a try in case it works easier. Sometimes I have found the bootstrap method to be a little bit tricky regards, Pablo. 2014-11-18 20:32 GMT+01:00 Kenneth Hoste <[email protected]>: > Hi Vali, > > On 18/11/14 20:21, Valeriu Codreanu wrote: > > Hello Kenneth, > > > > Thanks for your quick response. > > > > I actually realised that somehow there are two versions of environment > > modules on this system (3.1.6 and 3.2.10). > > > > When calling modulecmd ‹version I had indeed v3.2.10, but when calling > > module ‹version I had 3.1.6 because $MODULE_BIN was somehow pointing to > > that version. I have now changed $MODULE_BIN to point to the right > version > > but building Easybuild still does not work. I am pasting the output of > > some of the commands below: > > > > valeriuc@login3:~$ modulecmd --version > > VERSION=3.2.10 > > DATE=2012-12-21 > EasyBuild will use the 1st modulecmd binary that's in your $PATH, so > this should be OK. > This also explains why EasyBuild doesn't spit out a clear error message... > > It doesn't really care about the definition of the module function, as > long as it can find 'modulecmd' in there. > EasyBuild never uses 'module', it uses 'modulecmd' directly. > > So, something else must be going wrong... > > > <snip> > > > > +++ STAGE 2: installing EasyBuild in /home/valeriuc/.local/easybuild with > > EasyBuild from stage 1... > > > > > > > > > > == temporary log file in case of crash > > /scratch/easybuild-Lf9eCp/easybuild-AyXDqc.log > > Traceback (most recent call last): > > File "bootstrap_eb.py", line 584, in <module> > > main() > > File "bootstrap_eb.py", line 411, in main > > stage2(tmpdir, versions, install_path) > > File "bootstrap_eb.py", line 360, in stage2 > > easybuild_main() > > File > > > "/scratch/tmp17TPDz/eb_stage1/lib/python2.6/site-packages/easybuild_framewo > > rk-1.15.2-py2.6.egg/easybuild/main.py", line 279, in main > > modlist = session_module_list(testing=testing) > > File > > > "/scratch/tmp17TPDz/eb_stage1/lib/python2.6/site-packages/easybuild_framewo > > rk-1.15.2-py2.6.egg/easybuild/tools/testing.py", line 163, in > > session_module_list > > return modtool.list() > > File > > > "/scratch/tmp17TPDz/eb_stage1/lib/python2.6/site-packages/easybuild_framewo > > rk-1.15.2-py2.6.egg/easybuild/tools/modules.py", line 551, in list > > return self.run_module('list') > > File > > > "/scratch/tmp17TPDz/eb_stage1/lib/python2.6/site-packages/easybuild_framewo > > rk-1.15.2-py2.6.egg/easybuild/tools/modules.py", line 541, in run_module > > self.log.error(line) > > File > > > "/scratch/tmp17TPDz/eb_stage1/lib/python2.6/site-packages/easybuild_framewo > > rk-1.15.2-py2.6.egg/easybuild/tools/build_log.py", line 105, in error > > raise EasyBuildError(newMsg) > > easybuild.tools.build_log.EasyBuildError: 'EasyBuild crashed with an > error > > (at easybuild/tools/modules.py:541 in run_module): > > ModuleCmd_List.c(146):FATAL:996: The environment variables LOADEDMODULES > > and _LMFILES_ have inconsistent lengths.' > > > > > > I am also attaching the log file. > > > > What do you think I should check next? > > What does 'module list' print before you initiate the bootstrap? > > Can you set 'print_debug = True' in the bootstrap script, rerun the > bootstrap and provide us the full debug log? > > Do run the bootstrap with: > > python bootstrap_eb.py $HOME/.local/easybuild 2>&1 | tee eb_debug.log > > and then send us eb_debug.log.gz please. > > > regards, > > Kenneth > > > > > Thank you, > > Vali > > > > > > On 18/11/14 19:27, "Kenneth Hoste" <[email protected]> wrote: > > > >> Hello Vali, > >> > >> When using the Tcl/C version of environment modules, EasyBuild requires > >> v3.2.10 (i.e. the latest stable release). > >> > >> Although EasyBuild may work with slightly older versions, there are > >> known issues with v3.2.9 that may yield difficult to debug problems when > >> loading a large set of modules at once (which happens occasionally in an > >> EasyBuild context). > >> > >> Version 3.1.6 that you are still using is quite ancient, and thus > >> unsupported. > >> > >> I'm quite surprised that you didn't run into a clear error message, > >> since EasyBuild performs a version check on modulecmd. > >> What does "modulecmd --version" spit out with the version you're using? > >> > >> In any case: you'll need to upgrade to v3.2.10 of environment modules, > >> or look into using Lmod (http://sourceforge.net/projects/lmod/, v5.6.3 > >> or more recent is sufficient for EasyBuild v1.15.2). > >> > >> Installing environment modules v3.2.10 is quite easy, cfr. > >> > http://easybuild.readthedocs.org/en/latest/Installing-environment-modules- > >> without-root-permissions.html#installing-env-mod-c. > >> Likewise for Lmod, although that is a little bit more involved w.r.t. > >> the Lmod cache, etc. > >> > >> Do let us know if you have any further questions. > >> > >> > >> regards, > >> > >> Kenneth > >> > >> > >> On 18/11/14 15:23, [email protected] wrote: > >>> Hello, > >>> > >>> I wanted to try easy build on one of our systems. I tried to install it > >>> using > >>> the bootstrap method. However, when I run the script I get: > >>> > >>> valeriuc@login3:~/tmp$ python bootstrap_eb.py $HOME/.local/easybuild > >>> [[INFO]] Found module command 'modulecmd' (EnvironmentModulesC), so > >>> using it. > >>> [[INFO]] > >>> > >>> +++ STAGE 0: installing distribute via included (patched) > >>> distribute_setup.py... > >>> > >>> > >>> Downloading > >>> > >>> > http://pypi.python.org/packages/source/d/distribute/distribute-0.6.34.tar > >>> .gz > >>> Extracting in /scratch/tmpcU7_yb > >>> Now working in /scratch/tmpcU7_yb/distribute-0.6.34 > >>> Installing Distribute > >>> [[INFO]] > >>> > >>> +++ STAGE 1: installing EasyBuild in temporary dir with easy_install... > >>> > >>> > >>> Installing with setuptools.setup... > >>> Installing version 1.15.2 > >>> warning: install_lib: 'build/lib' does not exist -- no Python modules > to > >>> install > >>> zip_safe flag not set; analyzing archive contents... > >>> Installing with setuptools.setup... > >>> Installing version 1.15.2 (API version 1) > >>> Installing with setuptools.setup... > >>> Installing version 1.15.2 (required versions: API >= 1) > >>> Installing with setuptools.setup... > >>> Installing version 1.15.2.0 (required versions: API >= 1, easyblocks >= > >>> 1.15) > >>> warning: install_lib: 'build/lib' does not exist -- no Python modules > to > >>> install > >>> [[INFO]] > >>> > >>> +++ STAGE 2: installing EasyBuild in /home/valeriuc/.local/easybuild > >>> with > >>> EasyBuild from stage 1... > >>> > >>> > >>> == temporary log file in case of crash > >>> /scratch/easybuild-JZe8dh/easybuild- > >>> EF4Gm4.log > >>> Traceback (most recent call last): > >>> File "bootstrap_eb.py", line 584, in <module> > >>> main() > >>> File "bootstrap_eb.py", line 411, in main > >>> stage2(tmpdir, versions, install_path) > >>> File "bootstrap_eb.py", line 360, in stage2 > >>> easybuild_main() > >>> File "/scratch/tmpIu2dbb/eb_stage1/lib/python2.6/site-packages/ > >>> easybuild_framework-1.15.2-py2.6.egg/easybuild/main.py", line 279, in > >>> main > >>> modlist = session_module_list(testing=testing) > >>> File "/scratch/tmpIu2dbb/eb_stage1/lib/python2.6/site-packages/ > >>> easybuild_framework-1.15.2-py2.6.egg/easybuild/tools/testing.py", line > >>> 163, in > >>> session_module_list > >>> return modtool.list() > >>> File "/scratch/tmpIu2dbb/eb_stage1/lib/python2.6/site-packages/ > >>> easybuild_framework-1.15.2-py2.6.egg/easybuild/tools/modules.py", line > >>> 551, in > >>> list > >>> return self.run_module('list') > >>> File "/scratch/tmpIu2dbb/eb_stage1/lib/python2.6/site-packages/ > >>> easybuild_framework-1.15.2-py2.6.egg/easybuild/tools/modules.py", line > >>> 541, in > >>> run_module > >>> self.log.error(line) > >>> File "/scratch/tmpIu2dbb/eb_stage1/lib/python2.6/site-packages/ > >>> easybuild_framework-1.15.2-py2.6.egg/easybuild/tools/build_log.py", > >>> line 105, > >>> in error > >>> raise EasyBuildError(newMsg) > >>> easybuild.tools.build_log.EasyBuildError: 'EasyBuild crashed with an > >>> error (at > >>> easybuild/tools/modules.py:541 in run_module): > >>> ModuleCmd_List.c(146):FATAL:996: The environment variables > >>> LOADEDMODULES and > >>> _LMFILES_ have inconsistent lengths.' > >>> > >>> After I set up _LMFILES_ to the same value as LOADEDMODULES (probably > >>> not > >>> correct), EasyBuild installed. > >>> > >>> I can do: module load EasyBuild, and eb --help, but when I try to use > >>> EasyBuild to install a module I get: > >>> > >>> eb WRF-3.5.1-goolf-1.4.10-dmpar.eb -Dr > >>> == temporary log file in case of crash > >>> /scratch/easybuild-EZ0NgN/easybuild- > >>> LLd1gH.log > >>> ERROR: EasyBuild crashed with an error (at > easybuild/software/EasyBuild/ > >>> > 1.15.2/lib/python2.6/site-packages/easybuild_framework-1.15.2-py2.6.egg/ > >>> easybuild/tools/modules.py:541 in run_module): homkat(4):ERROR:154: > >>> Version > >>> symbol 'default' loops. > >>> > >>> I mention that I use the Tcl module environment, version 3.1.6. > >>> > >>> Could you please give me some hints on what could be wrong? > >>> > >>> Best regards, > >>> Vali > > -- Pablo Escobar López HPC systems engineer Biozentrum, University of Basel Swiss Institute of Bioinformatics SIB Email: [email protected] Phone: +41 61 267 21 80 http://www.biozentrum.unibas.ch
