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  • #16
    Poly-CH2 single threaded

    and it also occurs with the villin.
    Michael Larabel
    http://www.michaellarabel.com/

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    • #17
      -------------------------------------------------------
      Program mdrun_single, VERSION 3.3.3
      Source code file: gmxfio.c, line: 706

      Can not open file:
      topol.tpr
      -------------------------------------------------------



      Err I've now tried it with all four and they all fail.
      Michael Larabel
      http://www.michaellarabel.com/

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      • #18
        Oh dear. I'm not sure what's broken that.

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        • #19
          The tests all work for me.

          This is the problem:
          cd: 30: can't cd to /home/michael/pts-benchmark-env/md-gromacs/gmxbench/d.poly-ch2/
          It looks like the gmxbench-3.0.tar.gz isn't being extracted to the right place.

          Edit: I've tried it on another machine which is using the latest git code and it works fine too.
          Last edited by uncle_fungus; 05-07-2008, 02:24 PM. Reason: New info

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          • #20
            Hmmm I still can't get it working for me. I've wiped out everything and did a fresh install, etc.
            Michael Larabel
            http://www.michaellarabel.com/

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            • #21
              OK. I'll try it on a fresh install from git later on today.

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              • #22
                Just installed afresh from the latest git code and all the tests work fine for me.

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                • #23
                  So no other ideas then? I tried it on another box too and experienced the same failures.
                  Michael Larabel
                  http://www.michaellarabel.com/

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                  • #24
                    What distro are you using to test on?

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                    • #25
                      Ubuntu and it had worked in the same configuration with 0.1 and 0.2 of md-gromacs
                      Michael Larabel
                      http://www.michaellarabel.com/

                      Comment


                      • #26
                        OK, I know why. Ubuntu uses dash as it's /bin/sh and it looks like it doesn't support something I added in 0.3 (not sure what yet).

                        Edit: I know what the problem is, it's I/O redirection. Patch coming shortly.
                        Last edited by uncle_fungus; 05-09-2008, 08:33 AM.

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                        • #27
                          Patch for dash I/O redirection:

                          Code:
                          diff --git a/pts/test-resources/md-gromacs/install.sh b/pts/test-resources/md-gromacs/install.sh
                          index 40d3ec5..491f218 100644
                          --- a/pts/test-resources/md-gromacs/install.sh
                          +++ b/pts/test-resources/md-gromacs/install.sh
                          @@ -49,7 +49,7 @@ if [ -f $THIS_DIR/flopcount ]
                               rm -f $THIS_DIR/flopcount
                           fi
                           mkdir $THIS_DIR/gmxbench
                          -tar -xvf gmxbench-3.0.tar.gz -C $THIS_DIR/gmxbench/ &>/dev/null
                          +tar -xvf gmxbench-3.0.tar.gz -C $THIS_DIR/gmxbench/ 1>/dev/null 2>&1
                          
                           case "\$1" in
                           \"villin\")
                          @@ -75,12 +75,12 @@ esac
                          
                           case "\$2" in
                           \"mpi\")
                          -       $THIS_DIR/gromacs333_/bin/grompp -np \$NUM_CPU_CORES -nov &>/dev/null
                          -       $THIS_DIR/mpich2_/bin/mpiexec -np \$NUM_CPU_CORES $THIS_DIR/gromacs333_/bin/mdrun &> $THIS_DIR/flopcount
                          +       $THIS_DIR/gromacs333_/bin/grompp -np \$NUM_CPU_CORES -nov 1>/dev/null 2>&1
                          +       $THIS_DIR/mpich2_/bin/mpiexec -np \$NUM_CPU_CORES $THIS_DIR/gromacs333_/bin/mdrun 1>$THIS_DIR/flopcount 2>&1
                                  ;;
                           \"single-node\")
                          -       $THIS_DIR/gromacs333_/bin/grompp -nov &>/dev/null
                          -       $THIS_DIR/gromacs333_/bin/mdrun_single &> $THIS_DIR/flopcount
                          +       $THIS_DIR/gromacs333_/bin/grompp -nov 1>/dev/null 2>&1
                          +       $THIS_DIR/gromacs333_/bin/mdrun_single 1>$THIS_DIR/flopcount 2>&1
                                  ;;
                           *)
                                  exit

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                          • #28
                            Looks like that fixed it, thanks: http://global.phoronix-test-suite.co...0513-17000-220
                            Michael Larabel
                            http://www.michaellarabel.com/

                            Comment


                            • #29
                              Patch to add new *size info to profile (and change state to verified if that's ok).
                              Code:
                              diff --git a/pts/test-profiles/md-gromacs.xml b/pts/test-profiles/md-gromacs.xml
                              index 20da79f..bc08eea 100644
                              --- a/pts/test-profiles/md-gromacs.xml
                              +++ b/pts/test-profiles/md-gromacs.xml
                              @@ -4,8 +4,10 @@
                                              <TestType>Processor</TestType>
                                              <SoftwareType>Scientific</SoftwareType>
                                              <License>FREE</License>
                              -               <Status>UNVERIFIED</Status>
                              +               <Status>VERIFIED</Status>
                                              <Maintainer>Andrew Schofield</Maintainer>
                              +               <DownloadSize>30</DownloadSize>
                              +               <EnvironmentSize>231</EnvironmentSize>
                                      </TestProfile>
                                      <TestInformation>
                                              <Title>GROMACS MD Benchmark</Title>

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                              • #30
                                Should be in git shortly.
                                Michael Larabel
                                http://www.michaellarabel.com/

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