RE: [easybuild] EB for Intel Distribution for Python?

, 2017 10:00 AM To: easybuild@lists.ugent.be Subject: Re: [easybuild] EB for Intel Distribution for Python? On 01/19/2017 03:39 PM, Siddiqui, Shahzeb wrote: > Please see issue: > > https://github.com/hpcugent/easybuild-easyconfigs/issues/3922 > > I tried to build intel-python

RE: [easybuild] EB for Intel Distribution for Python?

: Re: [easybuild] EB for Intel Distribution for Python? On 01/20/2017 08:01 AM, Kenneth Hoste wrote: > > On 20/01/2017 14:56, Jack Perdue wrote: >> On 01/20/2017 07:31 AM, Siddiqui, Shahzeb wrote: >>> Ken, >>> >>> Can you have your team look into this issue

RE: [easybuild] Module File for Intel clck

Do you want me to update the PR with the name IntelClusterChecker. PATH variable needs to be set to use CLCK. -Original Message- From: easybuild-requ...@lists.ugent.be [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Kenneth Hoste Sent: Monday, February 20, 2017 5:05 AM To:

[easybuild] bcl2fastq2 easyblock help

Hello, I need to install bcl2fastq2 for a user and I was wondering if someone can help me get this working in EasyBuild. It uses a configure make to install the package, with a slight variation. The configure script is placed in inside a "src" directory and it doesn't build in current

[easybuild] Post Install Tests for EasyBuild

Hello, I am curious if anyone knows of any Testing framework that can run test for a particular application. In order for me to write test I have to learn the software and write appropriate test cases, this is very time-consuming. Similar to EasyBuild I am wondering if there is a tool to do

[easybuild] Module File for Intel clck

I am having trouble figuring out why IntelBase easyblock is generating this module file. Do I need to create a separate easyblock for this? The build works fine with the IntelBase easyblock when I added my sanity check path. hpcswadm@hpcv18$ml show clck

RE: [easybuild] EB for Intel Distribution for Python?

Hi Kenneth & Ole, Please see issue: https://github.com/hpcugent/easybuild-easyconfigs/issues/3922 I tried to build intel-python with IntelBase, it seems to be a trivial issue with license. Not sure how to fix this. Can you please provide input on this -Original Message- From:

[easybuild] MODULEPATH issue when supporting intel and intelcuda toolchain concurrently

Hello, I seem to notice an issue when building modules using HierarchicalNamingScheme when building out the intel and intelcuda toolchains. I notice that MODULEPATH is set for icc and ifort for intel directory. This is correct when setting up intel toolchain. hpcswadm@hpcv18$grep -iR

[easybuild] Easybuild as containers?

Hello, I would like to find out if there is a way to make Easybuild installs into containers. I am looking at ways to self-contain all the dependencies in container objects to properly deploy software packages and its dependencies. We are trying to build a software collection that contains all

RE: [easybuild] Easybuild as containers?

:21 PM Siddiqui, Shahzeb <shahzeb.siddi...@pfizer.com<mailto:shahzeb.siddi...@pfizer.com>> wrote: Hello, I would like to find out if there is a way to make Easybuild installs into containers. I am looking at ways to self-contain all the dependencies in container objects to properly deploy

RE: [easybuild] R extra packages

To: easybuild@lists.ugent.be Subject: Re: [easybuild] R extra packages On 12/16/2016 10:22 AM, Siddiqui, Shahzeb wrote: > > Hello, > > I would like to create a easyconfig for each R package, I find that to > be best suitable for our environment at Pfizer. I know we can pass > al

[easybuild] --extra-modules needed for changing module file

Hi, I need easybuild to manipulate the module file when building OpenMPI. I have OpenMPI built with LSF support, and we have a modulefile for lsf that we are using. Is there a way to load this module with -extra-modules but make it available when writing the module file. This option says it

[easybuild] RE: FPM issue

es => 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

RE: [easybuild] HDF5 build issue with lsf library libbat.so

requ...@lists.ugent.be] On Behalf Of Kenneth Hoste Sent: Monday, March 20, 2017 3:19 PM To: easybuild@lists.ugent.be Subject: Re: [easybuild] HDF5 build issue with lsf library libbat.so Hi Shahzeb, On 17/03/2017 20:20, Siddiqui, Shahzeb wrote: Hello, I am having a problem with building HDF5 that points to a

RE: [easybuild] GAMESS-US-20160818

: [easybuild] GAMESS-US-20160818 Hi Shahzeb, On 20/03/2017 21:25, Siddiqui, Shahzeb wrote: Hi, Does anyone have a working easyconfig of GAMESS preferably with foss or intel toolchain. I'm not aware of a recent easyconfig for GAMESS-US, other than the ones already included in EasyBuild (and available

[easybuild] Problem with NAMD, HDF5

Hello, I am looking for some help regarding these two issue. https://github.com/hpcugent/easybuild-easyconfigs/issues/4413 https://github.com/hpcugent/easybuild-easyconfigs/issues/4377 Regards, Shahzeb Siddiqui HPC Linux Engineer B2220-447.2 Groton, CT

[easybuild] eb file format toolchain version mismatch successful build?

Hello, I accidently did a build and I noticed easybuild went ahead with the build when I didn't have foss-2016a in the system but the file name was set that way but the toolchain name was set to foss-2016.03 which is my custom toolchain. I suspected that eb would check filename to make sure it

RE: [easybuild] HDF5 build issue with lsf library libbat.so

F5, but did > you try adding > > configopts = 'LIBS=-lm' > > to the HDF5 easyconfig? > > Markus > > > On 03/30/2017 09:21 PM, Siddiqui, Shahzeb wrote: >> Hello, >> >> >> >> I would really like if someone can assist me resolve the issue with &

[easybuild] matlab 2016b easybuild?

Hello, Does anyone happen to have a easyconfig for matlab 2016b. I am having trouble setting up a tarball correctly. I am getting an error as follows. I am pretty sure it's the way the tarball is setup. Anyone have any documentation for this. I recall my colleague having to install Matlab via

RE: [easybuild] RE: R-3.3.1-foss build error

, or GCCcore. From: Siddiqui, Shahzeb Sent: Tuesday, March 14, 2017 1:55 PM To: easybuild@lists.ugent.be Subject: RE: [easybuild] RE: R-3.3.1-foss build error The only difference I see is I am using binutils 2.27. I copied the files from GCC-5.4.0-2.26 and renamed the version. This is an issue I had

[easybuild] GAMESS-US-20160818

Hi, Does anyone have a working easyconfig of GAMESS preferably with foss or intel toolchain. If so can you please create a PR. Regards, Shahzeb Siddiqui HPC Linux Engineer B2220-447.2 Groton, CT

[easybuild] imkl log directory

Hello, I would like to find out if you know how to make sure imkl does a clean build. I am doing repetitive builds and sometimes I keep running into this issue where imkl fails at sanity check because it fails to clean up the directory. My tmp directory is set to /hpc/grid/scratch/easybuild.

RE: [easybuild] RE: R-3.3.1-foss build error

qu...@lists.ugent.be] On Behalf Of Kenneth Hoste Sent: Tuesday, March 14, 2017 12:41 PM To: easybuild@lists.ugent.be Subject: Re: [easybuild] RE: R-3.3.1-foss build error Hi Shahzeb, On 14/03/2017 17:27, Siddiqui, Shahzeb wrote: I think the problem I am having is a mixture of dependencies using GCC an

[easybuild] OpenMPI with LSF configuration

Hello, I want to find out if anyone has OpenMPI configured with LSF. If so I have a few questions. 1. Is LSF installed in a non-standard path? If so do you have LD_LIBRARY_PATH set for LSF_LIBDIR in your OpenMPI module file. 2. The profile.lsf sets up environment variable below,

[easybuild] LMOD error during sanity check

Hello, I have encountered this error in the past with several other packages. I couldn't figure out how to solve this error. It is strange because it works for some of my builds and fails for others. I was running these builds from Jenkins and it failed so I tried this via command line and got

RE: [easybuild] LMOD error during sanity check

suspect you have defined some custom properties or something in there, it might be good to double check that the module is sensible. On 17 March 2017 at 14:31, Ward Poelmans <wpoel...@gmail.com<mailto:wpoel...@gmail.com>> wrote: On 17-03-17 14:19, Siddiqui, Shahzeb wrote: > >

RE: [easybuild] HPC Testing Framework Collaboration

, I hope this gains traction into something useful. Regards, From: xavier.besse...@gmail.com [mailto:xavier.besse...@gmail.com] On Behalf Of Xavier Besseron Sent: Tuesday, March 14, 2017 6:57 PM To: easybuild@lists.ugent.be; Siddiqui, Shahzeb Subject: Re: [easybuild] HPC Testing Framework

[easybuild] Readthedocs EasyBuild dynamic data (program-output)

Hello, Our team is looking at Sphinx for documentation and we are hoping to use Readthedocs building the documentation. One feature we have is the ability to present dynamic data using program-output which runs a shell-script and presents the output in the document. We are running sphinx on

[easybuild] GPG signing RPM in EasyBuild

Hello, I want to find out if its possible to add a GPG signature to RPM via FPM. If so, I would like to utilize this feature. Regards, Shahzeb Siddiqui HPC Linux Engineer B2220-447.2 Groton, CT

RE: [easybuild] Readthedocs EasyBuild dynamic data (program-output)

Of Kenneth Hoste Sent: Thursday, April 6, 2017 6:12 AM To: easybuild@lists.ugent.be Subject: Re: [easybuild] Readthedocs EasyBuild dynamic data (program-output) On 04/04/2017 23:59, Siddiqui, Shahzeb wrote: Hello, Our team is looking at Sphinx for documentation and we are hoping to use Readthedoc

[easybuild] eb issues

Hello, Looking for some help from the community, I have a few issues still pending. https://github.com/hpcugent/easybuild-easyconfigs/issues/4446 https://github.com/hpcugent/easybuild-easyconfigs/issues/4443 https://github.com/hpcugent/easybuild-easyconfigs/issues/4413 Shahzeb Siddiqui HPC

[easybuild] BuildTest Framework initial-release

Hello, I would like to announce the release of buildtest - An automatic test generating framework. For those of you interested in automating your test procedures, please try this out and let me know your feedback. The intent is to start sharing

[easybuild] intelcuda issue

Hello, I am trying to build IntelCuda on RHEL 7.2 system, I am having a recursion issue. Has anyone else come across this issue, I want to find out if this is a eb bug or something to do with python or OS. I have tried to use system python, and both EB python and anaconda python. All three of

RE: [easybuild] MODULEPATH issue when supporting intel and intelcuda toolchain concurrently

rarchy-aware but definitely for other module tools). This can clearly lead to issues. Alan On 2 March 2017 at 15:32, Siddiqui, Shahzeb <shahzeb.siddi...@pfizer.com<mailto:shahzeb.siddi...@pfizer.com>> wrote: Hello, I seem to notice an issue when building modules using HierarchicalNam

[easybuild] GCCcore build in HMNS

Hello, I want to find out if the build for GCCcore 5.4.0 is suppose to look like this under HMNS. I have copied all the files from easybuild repo into my local directory because I have disabled robot paths. One thing I don't understand why there is M4 and binutils built with GCCcore toolchain

RE: [easybuild] HPC Testing Framework Collaboration

hursday, March 9, 2017 4:20 AM To: easybuild@lists.ugent.be Subject: Re: [easybuild] HPC Testing Framework Collaboration Hi Shahzeb, On 07/03/2017 17:31, Siddiqui, Shahzeb wrote: Hello, I have been working on creating a testing framework to automatically generate test cases for applications that

RE: [easybuild] HPC Testing Framework Collaboration

it?! enjoy, F. On Mar 7, 2017, at 4:31 PM, Siddiqui, Shahzeb <shahzeb.siddi...@pfizer.com> wrote: > Hello, > > I have been working on creating a testing framework to automatically generate > test cases for applications that work with EasyBuild in a HMNS module layout. > I coul

RE: [easybuild] RE: R-3.3.1-foss build error

LVShghg=v5g2JeJmmyOIaJFfII2nMBo_3-6t6pbdcWvsZNDLBkw=XZOuzfi7l-6vFS9P98NDTZP2ON5GT5IkSbwLhjlz27E=> regards, Kenneth On 11/03/2017 02:09, Siddiqui, Shahzeb wrote: Seems to be an issue with the nloptr package. It was not uncompressed properly. Any suggestions what to do? ython2.7/site-packages/vsc_base-2

[easybuild] R-3.3.1-foss build error

I seem to be having an issue building nloptr during the R build. I am using the R-3.3.1 with foss 2016. Any ideas how to fix this problem. == installing extension GGally 1.2.0 (291/414)... == installing extension beanplot 1.2 (292/414)... == installing extension clValid 0.6-6 (293/414)... ==

[easybuild] RE: R-3.3.1-foss build error

; exited with exitcode 1 and output: * installing *source == 2017-03-10 18:30:22,018 easyblock.py:276 INFO Closing log for application name R version 3.3.1 From: Siddiqui, Shahzeb Sent: Friday, March 10, 2017 8:07 PM To: easybuild@lists.ugent.be Subject: R-3.3.1-foss build error I seem to be having an

RE: [easybuild] GCCcore build in HMNS

olecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu<http://www.accre.vanderbilt.edu> On Mar 8 2017, at 12:58 pm, Siddiqui, Shahzeb <shahzeb.siddi...@pfizer.com<mailto:shahzeb.siddi...@pfizer.com&g

RE: [easybuild] RE: R-3.3.1-foss build error

t.be Subject: Re: [easybuild] RE: R-3.3.1-foss build error On 13/03/2017 16:52, Siddiqui, Shahzeb wrote: Hi, So now I was able to get further into my R build, that's great but I now encounter an issue with rgdal which seems to be an issue with PROJ. I think current version of rgdal requires PROJ 4.8.0 o

RE: [easybuild] GROMACS with gpu support

Oliver Stueker. He is actually working to modify the recipe for GROMACS GPU. Maybe he can help. Maxime On 17-03-01 14:38, Siddiqui, Shahzeb wrote: Hello, I am curious how I would build GROMACS with GPU support, I only see GROMACS build with multithreaded and hybrid approach. I notice th

[easybuild] GROMACS with gpu support

Hello, I am curious how I would build GROMACS with GPU support, I only see GROMACS build with multithreaded and hybrid approach. I notice this is just a tweak to toolchainopts that sets whether to build with openmp and mpi. This seems fine, but not sure how I would build with cuda. Do I need

RE: [easybuild] GROMACS with gpu support

I am putting you in contact with my colleague Oliver Stueker. He is > actually working to modify the recipe for GROMACS GPU. Maybe he can > help. > > Maxime > > On 17-03-01 14:38, Siddiqui, Shahzeb wrote: >>g >> Hello, >> >>

[easybuild] sanity check issue CUDA with GCC

Hello, I am puzzled why I am running into a issue when rebuilding CUDA with GCC support. It works fine when building with dummy toolchain. hpcswadm@hpcv18$eb CUDA-7.5.18-GCC-6.2.0.eb -r .. == temporary log file in case of crash /tmp/eb-ds88em/easybuild-YiC3Kf.log == resolving dependencies ...

[easybuild] gaussian build with eb

Hello, Anyone have a Gaussian g16 or g09 build with Easybuild. I can't seem to find any easyconfig in the repo or in the PR. Regards, Shahzeb Siddiqui HPC Linux Engineer B2220-447.2 Groton, CT

RE: [easybuild] GPG signing RPM in EasyBuild

nt: Monday, April 3, 2017 2:35 PM To: easybuild@lists.ugent.be Subject: Re: [easybuild] GPG signing RPM in EasyBuild On 03/04/2017 18:23, Siddiqui, Shahzeb wrote: Can we add the -rpm-sign feature to EasyBuild. It would also need a means to import gpg key. Similar to github token, if there is a flag -g

RE: [easybuild] HDF5 build issue with lsf library libbat.so

be fixed. It has nothing to do with HDF5 or anything else. Shared libraries are supposed to depend on all libraries they need, which in this case is -lm You should point this out to the person responsible for the libbat.so installation! On 03/31/2017 02:09 PM, Siddiqui, Shahzeb wrote: > I h

[easybuild] R-3.3.1-intel-2017 complete build

Hello guys, I have figured out how to build the 414 packages for R-3.3.1 from the eb file (https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb) There was an issue building rgdal, nloptr, and cairo. Rgdal was resolved by building with

RE: [EXTERNAL] Re: [easybuild] NWChem, Amber, OpenBabel, NAMD, GAMESS

Hi Maxime, It would be helpful to know which easyconfig file works for you for NWChem, Amber, OpenBabel, NAMD, and GAMESS-US. I checked out the repo, and I don’t know if there has been any changes. You have several branches so I am not sure which one I should be looking at. Regards, From:

[easybuild] RE: support for tmolex and tcoffee

I haven't heard any response. Does anyone have easyconfig for these packages that they mind sharing or submitting a pull request. Thanks From: easybuild-requ...@lists.ugent.be [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Siddiqui, Shahzeb Sent: Tuesday, June 6, 2017 2:20 PM

[easybuild] FW: fosscuda-2017a issue

that is in eb repo. I am doing my builds in Singularity, if you want to recreate the environment please see https://github.com/pescobar/singularity-easybuild Thanks From: Siddiqui, Shahzeb Sent: Monday, June 26, 2017 11:08 AM To: 'Vanzo, Davide' Subject: fosscuda-2017a issue Hi Davide, Please see

[easybuild] RE: eb in singularity

De: "Siddiqui, Shahzeb" <shahzeb.siddi...@pfizer.com<mailto:shahzeb.siddi...@pfizer.com>> À: easybuild@lists.ugent.be<mailto:easybuild@lists.ugent.be> Cc: "Gregory M. Kurtzer" <gmkurt...@gmail.com<mailto:gmkurt...@gmail.com>> E

RE: [easybuild] eb in singularity

ingularity. The latter worked really well and fast. So perhaps it makes sense to focus on integrating Docker builds into EB as one could deliver a more comprehensive solution to bigdata, devops and HPC people. Interested to hear some thoughts DP On Thu, May 4, 2017 at 9:53 A

[easybuild] eb in singularity

Hello folks, I would like to find out how Easybuild and Singularity are going to work together. I am trying to design an eb environment in Singularity as a container solution to host all of the eb apps in a prod environment. Is there anyone in the HPC community that is working on this?