Re: [easybuild] RE: FPM issue

2017-03-24 Thread Robert Schmidt 
Yeah, I'm pretty sure it was merged for 3.1.2. I broke the fpm call with
fixing it to be a command list. It is much safer for quote escaping this
way, but the exec call does the interpreter resolution and the /usr/bin/env
call gets in the way.

On Fri, Mar 24, 2017, 5:43 PM Siddiqui, Shahzeb 
wrote:

> It's 3.1.1
>
> Sent from my Android phone using TouchDown (www.symantec.com)
>
>
> -Original Message-
> *From:* Robert Schmidt [rjesc...@gmail.com]
> *Received:* Friday, 24 Mar 2017, 5:24PM
> *To:* easybuild@lists.ugent.be [easybuild@lists.ugent.be]
> *Subject:* Re: [easybuild] RE: FPM issue
>
> What version of easybuild is this? I think we fixed this in the newest
> version.
>
> On Fri, Mar 24, 2017 at 4:43 PM Siddiqui, Shahzeb <
> shahzeb.siddi...@pfizer.com> wrote:
>
> [hpcswadm@amrndhl1157 M4]$ eb M4-1.4.17.eb --rebuild --package
>
> == temporary log file in case of crash /tmp/eb-FXPNlB/easybuild-jyizZs.log
>
> == processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/M4/M4-1.4.17.eb
>
> == building and installing Core/M4/1.4.17.
> 
> ..
>
> == fetching files...
>
> == creating build dir, resetting environment...
>
> == unpacking...
>
> == patching...
>
> == preparing...
>
> == configuring...
>
> == building...
>
> == testing...
>
> == installing...
>
> == taking care of extensions...
>
> == postprocessing...
>
> == sanity checking...
>
> == cleaning up...
>
> == creating module...
>
> == permissions...
>
> == packaging...
>
> == FAILED: Installation ended unsuccessfully (build directory:
> /dev/shm/easybuild/build/M4/1.4.17/dummy-dummy): build failed (first 300
> chars): cmd "['/usr/bin/env', 'fpm', '--workdir',
> '/tmp/eb-FXPNlB/eb-pkgs-rqkJ_q', '--name', 'M4-1.4.17', '--provides',
> 'M4-1.4.17', '-t', 'rpm', '-s', 'dir', '--version', 'eb-3.1.1',
> '--iteration', '2', '--description', 'GNU M4 is an implementation of the
> traditional Unix macro processor.\n It is mostly SV
>
> == Results of the build can be found in the log file(s)
> /tmp/eb-FXPNlB/easybuild-M4-1.4.17-20170324.163735.zMGVv.log
>
> ERROR: Build of /hpc/hpcswadm/easybuild/M4/M4-1.4.17.eb failed (err:
> 'build failed (first 300 chars): cmd "[\'/usr/bin/env\', \'fpm\',
> \'--workdir\', \'/tmp/eb-FXPNlB/eb-pkgs-rqkJ_q\', \'--name\',
> \'M4-1.4.17\', \'--provides\', \'M4-1.4.17\', \'-t\', \'rpm\', \'-s\',
> \'dir\', \'--version\', \'eb-3.1.1\', \'--iteration\', \'2\',
> \'--description\', \'GNU M4 is an implementation of the traditional Unix
> macro processor.\\n It is mostly SV')
>
> [hpcswadm@amrndhl1157 M4]$ gem env
>
> RubyGems Environment:
>
>   - RUBYGEMS VERSION: 2.0.14
>
>   - RUBY VERSION: 2.0.0 (2014-11-13 patchlevel 598) [x86_64-linux]
>
>   - INSTALLATION DIRECTORY: /hpc/hpcswadm/.gem/ruby
>
>   - RUBY EXECUTABLE: /usr/bin/ruby
>
>   - EXECUTABLE DIRECTORY: /hpc/hpcswadm/bin
>
>   - RUBYGEMS PLATFORMS:
>
> - ruby
>
> - x86_64-linux
>
>   - GEM PATHS:
>
>  - /hpc/hpcswadm/.gem/ruby
>
>  - /usr/share/gems
>
>  - /usr/local/share/gems
>
>   - GEM CONFIGURATION:
>
>  - :update_sources => true
>
>  - :verbose => true
>
>  - :backtrace => false
>
>  - :bulk_threshold => 1000
>
>   - REMOTE SOURCES:
>
>  - https://rubygems.org/
> 
>
>
>
> *From:* Siddiqui, Shahzeb
> *Sent:* Friday, March 24, 2017 4:12 PM
> *To:* easybuild@lists.ugent.be
> *Subject:* FPM issue
>
>
>
> Hello,
>
>
>
> I can’t seem to figure out this issue. Help would be appreciated. This was
> working before now on a different system it is not. Previously I was using
> FPM 1.7.0. The error now happens with 1.8.1. I am not familiar with ruby so
> I am having trouble finding a solution
>
>
>
>
>
>
>
> == 2017-03-24 16:08:01,031 utilities.py:84 INFO Will be creating rpm
> package(s) in /tmp/eb-AVQd2M/eb-pkgs-xYRkaK
>
> == 2017-03-24 16:08:01,033 run.py:159 INFO running cmd: ['/usr/bin/env',
> 'fpm', '--workdir', '/tmp/eb-AVQd2M/eb-pkgs-xYRkaK', '--name', 'M4-1.4.17',
> '--provides', 'M4-1.4.17', '-t', 'rpm', '-s', 'dir', '--version',
> 'eb-3.1.1', '--iteration', '2', '--description', 'GNU M4 is an
> implementation of the traditional Unix macro processor.\n It is mostly SVR4
> compatible although it has some extensions \n (for example, handling more
> than 9 positional parameters to macros).\n GNU M4 also has built-in
> functions for including files, running shell commands, doing arithmetic,
> etc.\n', '--url', 'http://www.gnu.org/software/m4/m4.html
>

[easybuild] RE: FPM issue

2017-03-24 Thread Siddiqui, Shahzeb 
[hpcswadm@amrndhl1157 M4]$ eb M4-1.4.17.eb --rebuild --package
== temporary log file in case of crash /tmp/eb-FXPNlB/easybuild-jyizZs.log
== processing EasyBuild easyconfig /hpc/hpcswadm/easybuild/M4/M4-1.4.17.eb
== building and installing Core/M4/1.4.17...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== testing...
== installing...
== taking care of extensions...
== postprocessing...
== sanity checking...
== cleaning up...
== creating module...
== permissions...
== packaging...
== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/easybuild/build/M4/1.4.17/dummy-dummy): build failed (first 300 
chars): cmd "['/usr/bin/env', 'fpm', '--workdir', 
'/tmp/eb-FXPNlB/eb-pkgs-rqkJ_q', '--name', 'M4-1.4.17', '--provides', 
'M4-1.4.17', '-t', 'rpm', '-s', 'dir', '--version', 'eb-3.1.1', '--iteration', 
'2', '--description', 'GNU M4 is an implementation of the traditional Unix 
macro processor.\n It is mostly SV
== Results of the build can be found in the log file(s) 
/tmp/eb-FXPNlB/easybuild-M4-1.4.17-20170324.163735.zMGVv.log
ERROR: Build of /hpc/hpcswadm/easybuild/M4/M4-1.4.17.eb failed (err: 'build 
failed (first 300 chars): cmd "[\'/usr/bin/env\', \'fpm\', \'--workdir\', 
\'/tmp/eb-FXPNlB/eb-pkgs-rqkJ_q\', \'--name\', \'M4-1.4.17\', \'--provides\', 
\'M4-1.4.17\', \'-t\', \'rpm\', \'-s\', \'dir\', \'--version\', \'eb-3.1.1\', 
\'--iteration\', \'2\', \'--description\', \'GNU M4 is an implementation of the 
traditional Unix macro processor.\\n It is mostly SV')
[hpcswadm@amrndhl1157 M4]$ gem env
RubyGems Environment:
  - RUBYGEMS VERSION: 2.0.14
  - RUBY VERSION: 2.0.0 (2014-11-13 patchlevel 598) [x86_64-linux]
  - INSTALLATION DIRECTORY: /hpc/hpcswadm/.gem/ruby
  - RUBY EXECUTABLE: /usr/bin/ruby
  - EXECUTABLE DIRECTORY: /hpc/hpcswadm/bin
  - RUBYGEMS PLATFORMS:
- ruby
- x86_64-linux
  - GEM PATHS:
 - /hpc/hpcswadm/.gem/ruby
 - /usr/share/gems
 - /usr/local/share/gems
  - GEM CONFIGURATION:
 - :update_sources => true
 - :verbose => true
 - :backtrace => false
 - :bulk_threshold => 1000
  - REMOTE SOURCES:
 - https://rubygems.org/

From: Siddiqui, Shahzeb
Sent: Friday, March 24, 2017 4:12 PM
To: easybuild@lists.ugent.be
Subject: FPM issue

Hello,

I can't seem to figure out this issue. Help would be appreciated. This was 
working before now on a different system it is not. Previously I was using FPM 
1.7.0. The error now happens with 1.8.1. I am not familiar with ruby so I am 
having trouble finding a solution



== 2017-03-24 16:08:01,031 utilities.py:84 INFO Will be creating rpm package(s) 
in /tmp/eb-AVQd2M/eb-pkgs-xYRkaK
== 2017-03-24 16:08:01,033 run.py:159 INFO running cmd: ['/usr/bin/env', 'fpm', 
'--workdir', '/tmp/eb-AVQd2M/eb-pkgs-xYRkaK', '--name', 'M4-1.4.17', 
'--provides', 'M4-1.4.17', '-t', 'rpm', '-s', 'dir', '--version', 'eb-3.1.1', 
'--iteration', '2', '--description', 'GNU M4 is an implementation of the 
traditional Unix macro processor.\n It is mostly SVR4 compatible although it 
has some extensions \n (for example, handling more than 9 positional parameters 
to macros).\n GNU M4 also has built-in functions for including files, running 
shell commands, doing arithmetic, etc.\n', '--url', 
'http://www.gnu.org/software/m4/m4.html', '--exclude', 
'nfs/grid/software/testing/RHEL7/easybuild/software/Core/M4/1.4.17/easybuild/*.log',
 '--exclude', 
'nfs/grid/software/testing/RHEL7/easybuild/software/Core/M4/1.4.17/easybuild/*.md',
 '/nfs/grid/software/testing/RHEL7/easybuild/software/Core/M4/1.4.17', 
'/nfs/grid/software/testing/RHEL7/easybuild/modules/all/Core/M4/1.4.17.lua']
== 2017-03-24 16:08:01,080 build_log.py:147 ERROR EasyBuild crashed with an 
error (at 
easybuild/software/EasyBuild/3.1.1/lib/python2.7/site-packages/vsc_base-2.5.7-py2.7.egg/vsc/utils/exceptions.py:124
 in __init__): cmd "['/usr/bin/env', 'fpm', '--workdir', 
'/tmp/eb-AVQd2M/eb-pkgs-xYRkaK', '--name', 'M4-1.4.17', '--provides', 
'M4-1.4.17', '-t', 'rpm', '-s', 'dir', '--version', 'eb-3.1.1', '--iteration', 
'2', '--description', 'GNU M4 is an implementation of the traditional Unix 
macro processor.\n It is mostly SVR4 compatible although it has some extensions 
\n (for example, handling more than 9 positional parameters to macros).\n GNU 
M4 also has built-in functions for including files, running shell commands, 
doing arithmetic, etc.\n', '--url', 'http://www.gnu.org/software/m4/m4.html', 
'--exclude', 
'nfs/grid/software/testing/RHEL7/easybuild/software/Core/M4/1.4.17/easybuild/*.log',
 '--exclude', 
'nfs/grid/software/testing/RHEL7/easybuild/software/Core/M4/1.4.17/easybuild/*.md',
 '/nfs/grid/software/testing/RHEL7/easybuild/software/Core/M4/1.4.17', 
'/nfs/grid/software/testing/RHEL7/easybuild/modules/all/Core/M4/1.4.17.lua']" 
exited with exitcode 2 and output:
/usr/local/bin/fpm: line 9: require: command not found
/usr/local/bin/fpm: line 11: version:

Re: [easybuild] Lmod integration - Families

2017-03-24 Thread Vanzo, Davide 
I am using intel-2016b.
However, it comes out is is an Lmod problem. I get the same message when I try 
to load the hidden module intel/.2016b. But I cannot figure out why. I will ask 
on the Lmod list.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

On Mar 24 2017, at 3:26 am, Markus Geimer  wrote:

Davide,

> I am using your SwatHMNS module and everything is working fine until I
> try to build something that requires the imkl module. The error I see is
> the following:
>
> Lmod has detected the following error: These module(s) exist but cannot be
> loaded as requested: "imkl/11.3.3.210", "IntelMPI/5.1.3.181"
>
> It looks like EB is trying to load the IntelMPI and imkl in the opposite
> order. If I manually try to load the (hidden) intel/2016b module
> everything gets loaded correctly. Any idea?

Which toolchain are you using? The order in which the
dependencies are listed in the toolchain easyconfig should
be the order in which modules are loaded. If not, we are
in trouble (I think)...

Markus

--
Dr. Markus Geimer
Juelich Supercomputing Centre
Institute for Advanced Simulation
Forschungszentrum Juelich GmbH
52425 Juelich, Germany

Phone: +49-2461-61-1773
Fax: +49-2461-61-6656
E-mail: m.gei...@fz-juelich.de
WWW: http://www.fz-juelich.de/jsc/



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt