fasrc / helmod Goto Github PK

The symbolic link that I suspect was accidentally added breaks the project for people not having the target directory on their system. Can you please remove the symbolic link and switch it back to an empty directory. It looks like this has happened a few times before.

Reading the install notes:
https://github.com/fasrc/helmod/blob/master/doc/INSTALL.md

I just wanted to double check if there are any compatibility issues with using newer Lmod version 7

We started evaluating using helmod on our cluster and it was working really well until I tried getting trinity rna-seq installed which had a lmod dependency on trinity perl-modules-5.10.1-fasrc11.spec. How does one actually get perl-modules-5.10.1-fasrc11.spec compiled? Many of the module versions are not available via cpan and it was tedious to say the least in getting them downloaded. I made a gcb01 release and updated the spec file with some versions of modules that I had to download newer versions of but I couldn't get a clean compile. Would it be possible for someone with more inside experience to take a look at the health of the perl-modules-5.10.1-fasrc11.spec or possible give us the ability to download from your SOURCES to get past this bump in the road? Could be that I'm missing something about getting perl-modules-5.10.1-fasrc11.spec compiled. If someone replies to this I'll get your the errors I was encountering while attempting to build my own version of perl-modules with some slightly newer module versions.

On the install doc:

The HeLmod system is designed to work on a CentOS 6 cluster. If you're setting this up for an organization other than Harvard FAS Research Computing (@fasrc on github), create a new canonical HeLmod master remote and adjust urls below accordingly.

Is support for CentOS 7 available/tested? Our group at Johns Hopkins is interested in trying this tool out.

Thanks!
Kevin at MARCC (Maryland Advanced Research Computing Center)

I am trying to build the kallisto-0.42.4-fasrc02 module. Both dependency modules are in place and working. The build gets to the cmake step, but does not progress beyond '-- The C compiler identification is GNU 4.4.7' - it has stuck at this point for several days. Added '--debug-output' to the cmake command in the spec file to try to get more info, which yielded:

• cmake --debug-output -DCMAKE_INSTALL_PREFIX=/nfs/software/helmod/apps/Core/kallisto/0.42.4-fasrc02 '-DCMAKE_INCLUDE_PATH:STRING=/nfs/software/helmod/apps/Core/hdf5/1.8.12-fasrc08/include;/nfs/software/helmod/apps/Core/zlib/1.2.8-fasrc05/include' '-DCMAKE_LIBRARY_PATH:STRING=/nfs/software/helmod/apps/Core/zlib/1.2.8-fasrc05/lib;/nfs/software/helmod/apps/Core/hdf5/1.8.12-fasrc08/lib64' ..
  Running with debug output on.
  -- The C compiler identification is GNU 4.4.7
  Called from: [2] /nfs/software/helmod/apps/Core/cmake/2.8.12.2-fasrc01/share/cmake-2.8/Modules/CMakeDetermineCCompiler.cmake
  [1] /home/dss13/helmod/rpmbuild/BUILD/kallisto-0.42.4/CMakeLists.txt

and has been stuck at that point since. 'ps' shows cmake running with state R+, using CPU. I have used this cmake module successfully in the past so do not suspect an issue with that dependency. Any insight as to what may be going on here would be very much appreciated.