Hi Jens and list: I have attached the scripts I used to build VOTCA, and the resulting log files. I called the scripts like `source build.intel.sh &> log.build.intel`. The build fails without the options to disable Intel MKL, the 'intel' files, with either 1 process (./build.sh -j1) or many processes (e.g. ./build.sh -j12, or without -j option). The build succeeds with the options to disable Intel MKL (-DWITH_MKL=OFF -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON), the 'no-intel' files, again regardless of how many processes.
When I reported the problem it was the 1.4 release, but now it looks like it's 1.5-dev. This is on one of our HPC clusters, an SGI ICE X machine. Let me know if I can provide any other information. Cheers, Robert On Monday, January 23, 2017 at 10:27:31 AM UTC-5, Robert Elder wrote: > > The machine I was using to build is down at the moment, but I'll send a > build log when I can. > > Cheers, > Robert > > On Friday, January 20, 2017 at 1:15:54 PM UTC-5, [email protected] wrote: >> >> Hi Robert, >> >> I was unable to reproduce the error. May you send me the complete build >> log? >> >> Cheers >> >> Jens >> >> Am Donnerstag, 19. Januar 2017 19:01:23 UTC+1 schrieb Robert Elder: >>> >>> Hi Users: >>> >>> I just wanted to share a Votca compilation problem and solution I >>> encountered recently. When running the build.sh script, as described here ( >>> https://github.com/votca/csg/wiki/Installing#from-source), I >>> encountered this error: >>> >>> [snip] >>> >>> cleaning tools >>> buidling tools >>> Scanning dependencies of target votca_tools_manpages >>> [ 0%] Built target votca_tools_manpages >>> Scanning dependencies of target intel >>> Scanning dependencies of target gitversion >>> Current git revision is 7ca4a6d >>> [ 0%] Built target gitversion >>> Scanning dependencies of target votca_tools >>> [ 2%] Creating directories for 'intel' >>> [ 4%] Performing download step (download, verify and extract) for >>> 'intel' >>> [ 7%] -- downloading... >>> src=' >>> http://software.intel.com/sites/default/files/managed/76/8c/intel-mkl-and-boost-example.zip >>> ' >>> dst= >>> '/p/home/elderr/src/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip' >>> timeout='none' >>> [ 9%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/ >>> datacollection.cc.o >>> CMake Error at intel-stamp/download-intel.cmake:9 (file): >>> file DOWNLOAD HASH mismatch >>> >>> for file: [/p/home/elderr/src/votca/src/tools/intel/src/intel-mkl- >>> and-boost-example.zip] >>> expected hash: [b957ee63a2167ad21b650b47726cd55c] >>> actual hash: [d41d8cd98f00b204e9800998ecf8427e] >>> >>> >>> >>> make[2]: *** [intel/src/intel-stamp/intel-download] Error 1 >>> make[1]: *** [CMakeFiles/intel.dir/all] Error 2 >>> make[1]: *** Waiting for unfinished jobs.... >>> >>> [snip] >>> >>> Basically CMake failed because the hashes on >>> intel-mkl-and-boost-example.zip did not match -- the reason being that the >>> downloaded intel-mkl-and-boost-example.zip was a zero byte file! I have no >>> idea why; perhaps some obscure problem on our machine. I don't know CMake >>> well enough, but it seems to be running with multiple threads -- maybe a >>> race condition on download vs. hash? Just speculation. >>> >>> Anyway I solved this by downloading the 'src' file from >>> http://software.intel.com manually and putting it in the required >>> location ('dst'). Then I reran the build script, it picked up where it left >>> off and completed without a problem. >>> >>> Hopefully that helps someone. Thanks for this great tool! >>> -Robert Elder >>> >> -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
#!/bin/bash
export CC=icc
export CXX=icpc
export BOOST_ROOT=$HOME
export FFTW3_INCLUDE_DIR=$HOME/include
export FFTW3_LIBRARY=$HOME/lib/libfftw3.so
export GSL_INCLUDE_DIR=$HOME/include
export GSL_LIBRARY=$HOME/lib/libgsl.so
export GSLCBLAS_LIBRARY=$HOME/lib/libgslcblas.so
export GROMACS_INCLUDE_DIR=$HOME/include/gromacs
export GROMACS_LIBRARY=$HOME/lib64/libgromacs_mpi.so
export EXPAT_INCLUDE_DIR=$HOME/include
export EXPAT_LIBRARY=$HOME/lib/libexpat.so
prefix=$HOME/src/votca-test
mkdir -p ${prefix}/src
cd ${prefix}/src
wget https://raw.githubusercontent.com/votca/buildutil/master/build.sh
chmod +x build.sh
./build.sh -j12 --prefix ${prefix} -ud tools csg -DFFTW3_LIBRARY=$FFTW3_LIBRARY -DFFTW3_INCLUDE_DIR=$FFTW3_INCLUDE_DIR -DGSL_INCLUDE_DIR=$GSL_INCLUDE_DIR -DGSL_LIBRARY=$GSL_LIBRARY -DGSLCBLAS_LIBRARY=$GSLCBLAS_LIBRARY -DGROMACS_INCLUDE_DIR=$GROMACS_INCLUDE_DIR -DGROMACS_LIBRARY=$GROMACS_LIBRARY -DEXPAT_INCLUDE_DIR=$EXPAT_INCLUDE_DIR -DEXPAT_LIBRARY=$EXPAT_LIBRARY -DWITH_SQLITE3=OFF -DBoost_INCLUDE_DIR=$HOME/include -DBoost_PROGRAM_OPTIONS_LIBRARY=$HOME/lib/libboost_program_options.so -DBoost_FILESYSTEM_LIBRARY=$HOME/lib/libboost_filesystem.so -DBoost_SYSTEM_LIBRARY=$HOME/lib/libboost_system.so
#!/bin/bash
export CC=icc
export CXX=icpc
export BOOST_ROOT=$HOME
export FFTW3_INCLUDE_DIR=$HOME/include
export FFTW3_LIBRARY=$HOME/lib/libfftw3.so
export GSL_INCLUDE_DIR=$HOME/include
export GSL_LIBRARY=$HOME/lib/libgsl.so
export GSLCBLAS_LIBRARY=$HOME/lib/libgslcblas.so
export GROMACS_INCLUDE_DIR=$HOME/include/gromacs
export GROMACS_LIBRARY=$HOME/lib64/libgromacs_mpi.so
export EXPAT_INCLUDE_DIR=$HOME/include
export EXPAT_LIBRARY=$HOME/lib/libexpat.so
prefix=$HOME/src/votca-test-no-intel
mkdir -p ${prefix}/src
cd ${prefix}/src
wget https://raw.githubusercontent.com/votca/buildutil/master/build.sh
chmod +x build.sh
./build.sh -j1 --prefix ${prefix} -ud tools csg -DFFTW3_LIBRARY=$FFTW3_LIBRARY -DFFTW3_INCLUDE_DIR=$FFTW3_INCLUDE_DIR -DGSL_INCLUDE_DIR=$GSL_INCLUDE_DIR -DGSL_LIBRARY=$GSL_LIBRARY -DGSLCBLAS_LIBRARY=$GSLCBLAS_LIBRARY -DGROMACS_INCLUDE_DIR=$GROMACS_INCLUDE_DIR -DGROMACS_LIBRARY=$GROMACS_LIBRARY -DEXPAT_INCLUDE_DIR=$EXPAT_INCLUDE_DIR -DEXPAT_LIBRARY=$EXPAT_LIBRARY -DWITH_SQLITE3=OFF -DBoost_INCLUDE_DIR=$HOME/include -DBoost_PROGRAM_OPTIONS_LIBRARY=$HOME/lib/libboost_program_options.so -DBoost_FILESYSTEM_LIBRARY=$HOME/lib/libboost_filesystem.so -DBoost_SYSTEM_LIBRARY=$HOME/lib/libboost_system.so -DWITH_MKL=OFF -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON
log.build.no-intel
Description: Binary data
log.build.intel
Description: Binary data
