Merge remote-tracking branch 'upstream/master_pre_stage' into fix_typos

INSTALL.md

@@ -287,18 +287,17 @@ Remarks:
   - you should specify compiler flags for Intel Fortran compiler; in the example only "-O3 -xAVX2" is set
   - you should be carefull with the CFLAGS, the example shows typical flags
 
-FC=wrapper_for_intel_compiler ./configure FCFLAGS="-O3 -xAVX2" CFLAGS="-O3 -march=native -mavx2 -mfma funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" --enable-option-checking=fatal SCALAPACK_LDFLAGS="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64"
+FC=mpi_wrapper_for_intel_Fortran_compiler CC=mpi_wrapper_for_gnu_C_compiler ./configure FCFLAGS="-O3 -xAVX2" CFLAGS="-O3 -march=native -mavx2 -mfma -funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" --enable-option-checking=fatal SCALAPACK_LDFLAGS="L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64"
 
 
 2. Building with GNU Fortran compiler and GNU C compiler:
 
-Remarks:
-  - you have to know the name of the GNU Fortran compiler wrapper
-  - you do not have to specify a C compiler (with CC); GNU C compiler is recognized automatically
-  - you should specify compiler flags for GNU Fortran compiler; in the example "-O3 -march=native -mavx2 -mfma funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" is set
-  - you should be carefull with the CFLAGS, the example shows typical flags
+Remarks: - you have to know the name of the GNU Fortran compiler wrapper
+         - you DO have to specify a C compiler (with CC); GNU C compiler is recognized automatically
+	 - you should specify compiler flags for GNU Fortran compiler; in the example only "-O3 -march=native -mavx2 -mfma" is set
+	 - you should be carefull with the CFLAGS. The example shows typical flags
 
-FC=wrapper_for_gnu_compiler ./configure FCFLAGS="-O3 -march=native -mavx2 -mfma" CFLAGS="-O3 -march=native -mavx2 -mfma funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" --enable-option-checking=fatal SCALAPACK_LDFLAGS="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64"
+FC=mpi_wrapper_for_gnu_Fortran_compiler CC=mpi_wrapper_for_gnu_C_compiler ./configure FCFLAGS="-O3 -march=native -mavx2 -mfma" CFLAGS="-O3 -march=native -mavx2 -mfma  -funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" --enable-option-checking=fatal SCALAPACK_LDFLAGS="L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64"
 
 
 2. Building with Intel Fortran compiler and Intel C compiler:
@@ -309,7 +308,7 @@ Remarks:
   - you should specify compiler flags for Intel Fortran compiler; in the example only "-O3 -xAVX2" is set
   - you should be carefull with the CFLAGS, the example shows typical flags
 
-FC=wrapper_for_intel_compiler CC=icc ./configure FCFLAGS="-O3 -xAVX2" CFLAGS="-O3 -xAVX2" --enable-option-checking=fatal SCALAPACK_LDFLAGS="-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64"
+FC=mpi_wrapper_for_intel_Fortran_compiler CC=mpi_wrapper_for_intel_C_compiler ./configure FCFLAGS="-O3 -xAVX2" CFLAGS="-O3 -xAVX2" --enable-option-checking=fatal SCALAPACK_LDFLAGS="L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64"
 
 
 

ci_test_scripts/.ci-env-vars

+
+
+if [ "$(hostname)" == "freya01" ]; then module purge && source /mpcdf/SLE_12_SP3/try_new_modules.sh && module load git intel/17.0 gcc/7 impi/2017.3  mkl/2017.3 autoconf automake libtool pkg-config; fi
+
 if [ "$(hostname)" == "buildtest-rzg" ]; then module load impi/5.1.3 intel/16.0 gcc/6.3 mkl/11.3 autotools pkg-config; fi
 
 if [ "$(hostname)" == "knl1" -o "$(hostname)" == "knl2" -o "$(hostname)" == "knl3" -o "$(hostname)" == "knl4" ] ; then module load impi/2017.4 intel/17.0 gcc/7.2 mkl/2017 pkg-config; fi

ci_test_scripts/configure_step.sh

 #!/bin/bash
 source /etc/profile.d/modules.sh
 set -ex
-pwd
 
 source ./ci_test_scripts/.ci-env-vars
 echo $1

ci_test_scripts/run_ci_tests.sh

@@ -12,6 +12,7 @@ ompThreads=1
 configueArg=""
 skipStep=0
 batchCommand=""
+interactiveRun="yes"
 
 function usage() {
 	cat >&2 <<-EOF
@@ -19,7 +20,7 @@ function usage() {
 		Call all the necessary steps to perform an ELPA CI test
 
 		Usage:
-		  run_ci_tests [-c configure arguments] [-j makeTasks] [-h] [-t MPI Tasks] [-m matrix size] [-n number of eigenvectors] [-b block size] [-o OpenMP threads] [-s skipStep] [-q submit command]
+		  run_ci_tests [-c configure arguments] [-j makeTasks] [-h] [-t MPI Tasks] [-m matrix size] [-n number of eigenvectors] [-b block size] [-o OpenMP threads] [-s skipStep] [-q submit command] [-i interactive run]
 
 		Options:
 		 -c configure arguments
@@ -48,13 +49,16 @@ function usage() {
 		 -q submit command
 		    Job steps will be submitted via command to a batch system (default no submission)
 
+		 -i interactive_run
+		    if "yes" NO no batch command will be triggered
+
 		 -h
 		    Print this help text
 	EOF
 }
 
 
-while getopts "c:t:j:m:n:b:o:s:q:h" opt; do
+while getopts "c:t:j:m:n:b:o:s:q:i:h" opt; do
 	case $opt in
 		j)
 			makeTasks=$OPTARG;;
@@ -74,6 +78,8 @@ while getopts "c:t:j:m:n:b:o:s:q:h" opt; do
 			skipStep=$OPTARG;;
 		q)
 			batchCommand=$OPTARG;;
+		i)
+			interactiveRun=$OPTARG;;
 		:)
 			echo "Option -$OPTARG requires an argument" >&2;;
 		h)
@@ -89,24 +95,25 @@ then
   echo "Skipping the test since option -s has been specified"
   exit 0
 else
-  echo  $batchCommand
   if [ "$batchCommand" == "srun" ]
   then
-    echo "Running with $batchCommand with $SRUN_COMMANDLINE_CONFIGURE"
-#    $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=1 $SRUN_COMMANDLINE_CONFIGURE bash -c ' {source /etc/profile.d/modules.sh && source ./ci_test_scripts/ci-env-vars && eval  ./configure $configureArgs; }'
-    $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=1 $SRUN_COMMANDLINE_CONFIGURE ./ci_test_scripts/configure_step.sh "$configureArgs"
-
-    if [ $? -ne 0 ]; then cat config.log && exit 1; fi
-    sleep 1
-    $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=8 $SRUN_COMMANDLINE_BUILD ./ci_test_scripts/build_step.sh $makeTasks
-    if [ $? -ne 0 ]; then exit 1; fi
-    sleep 1
-    $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=2 $SRUN_COMMANDLINE_RUN ./ci_test_scripts/test_step.sh $mpiTasks $ompThreads "TEST_FLAGS=\" $matrixSize $nrEV $blockSize \" "
-    if [ $? -ne 0 ]; then exit 1; fi
-
-    grep -i "Expected %stop" test-suite.log && exit 1 || true ;
-    if [ $? -ne 0 ]; then exit 1; fi
-
+    if [ "$interactiveRun" == "no" ]
+    then
+      echo "Running with $batchCommand with $SRUN_COMMANDLINE_CONFIGURE"
+#      $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=1 $SRUN_COMMANDLINE_CONFIGURE bash -c ' {source /etc/profile.d/modules.sh && source ./ci_test_scripts/ci-env-vars && eval  ./configure $configureArgs; }'
+      $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=1 $SRUN_COMMANDLINE_CONFIGURE ./ci_test_scripts/configure_step.sh "$configureArgs"
+
+      if [ $? -ne 0 ]; then cat config.log && exit 1; fi
+      sleep 1
+      $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=8 $SRUN_COMMANDLINE_BUILD ./ci_test_scripts/build_step.sh $makeTasks
+      if [ $? -ne 0 ]; then exit 1; fi
+      sleep 1
+      $batchCommand --ntasks-per-core=1 --ntasks=1 --cpus-per-task=2 $SRUN_COMMANDLINE_RUN ./ci_test_scripts/test_step.sh $mpiTasks $ompThreads "TEST_FLAGS=\" $matrixSize $nrEV $blockSize \" "
+      if [ $? -ne 0 ]; then exit 1; fi
+
+      grep -i "Expected %stop" test-suite.log && exit 1 || true ;
+      if [ $? -ne 0 ]; then exit 1; fi
+    fi
   else
     #eval ./configure $configureArgs
     ./ci_test_scripts/configure_step.sh "$configureArgs"

nvcc_wrap

 #!/bin/sh
 
-$NVCC `echo $@ | sed 's/-fPIC/-Xcompiler -fPIC/'`
+$NVCC `echo $@ | sed 's/-fPIC/-Xcompiler -fPIC/; s/-Wl/-Xlinker -Wl/; '`