Home Forums Installation Running the testSuite on cluster Hebbe (Sweden)

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  • Carlo Negrato
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    Hi all ,
    after installation of ReFRESCO on cluster Hebbe, (the tag 2.4.0) , I have run the testSuite. The problems encountered are presented here; some of you may have comments, or find this thread useful for their specific machine as well.

    First, some modules are loaded (in .bashrc for instance) :
    module load intel/2017b
    module load ifort/2017.1.132-GCC-6.3.0-2.27
    module load icc/2017.1.132-GCC-6.3.0-2.27
    module load impi/2017.1.132
    module load CMake
    module load Doxygen/1.8.13
    module load Python/2.7.13
    module load matplotlib/2.0.2-Python-2.7.13-Qt-4.8.7

    Secondly, Gnuplot and matplotlib modules are required to run the testSuite. However, because of the inconvenient toolchain on Hebbe, they cannot be loaded simultaneously…!! the only solution I could think of is to install gnuplot locally. To-date , it can be found here:
    https://sourceforge.net/projects/gnuplot/files/gnuplot/
    Make sure you install gnuplot 4.6.x, NOT higher, as written also in MODS. The installation options are described in the documentation coming with the tarball. In short, two line are needed. The first is my user-specific installation folder:
    ./configure –prefix=/c3se/users/negrato/Hebbe/Soft/gnuplot-4.6.6-install
    make install

    Then, I experienced the following errors when running the “make postpro” command:
    —-
    ERROR:root:code for hash md5 was not found.
    ValueError: unsupported hash type md5
    ERROR:root:code for hash sha1 was not found
    ValueError: unsupported hash type sha1
    —-
    and several other similar errors.
    I guess the problem was a conflicting path, because this was solved by changing one line in the refresco-dev-tag2.4.0.sh script:
    #export LD_LIBRARY_PATH=$HDF5_DIR/lib:$PETSC_DIR/lib:$LICENSING_DIR/boost/lib64:$LICENSING_DIR/sll/lib64:$LD_LIBRARY_PATH
    export LD_LIBRARY_PATH=$HDF5_DIR/lib:$PETSC_DIR/lib:$LD_LIBRARY_PATH

    Then, on Hebbe the TeX commands are available only through a singularity box. Which means that some lines must be changed both in tables.sh as well as extra_postpro.sh scripts:
    # latex tables.tex
    singularity exec /apps/Singularity/latex.simg latex tables.tex
    # dvips -t landscape tables.dvi -o tables.ps
    singularity exec /apps/Singularity/latex.simg dvips -t landscape tables.dvi -o tables.ps
    Of course, one could set an alias for these… However, for some reasons obscure to me, I was not able to set aliases:
    alias latex=’singularity exec /apps/Singularity/latex.simg latex’
    does not work with single nor with double quotes. Any suggestion here ??

    Finally, a2ps is not installed on Hebbe. Again, a local installation will do the trick . To-date a2ps can be downloaded from:
    http://ftp.gnu.org/gnu/a2ps/
    and then do the following (the first line is my local folder) :
    ./configure –prefix=/c3se/users/negrato/Hebbe/Soft/a2ps/a2ps-4.14-install
    make install

    After that, the testSuite can be run (all of the make pre – make compute – make postpro targets)
    Carlo

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