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MPIBP-Hummer
BioEM
Commits
67c620e2
Commit
67c620e2
authored
Jun 16, 2016
by
Markus Rampp
Browse files
CI: restructure .gitlab-ci.yml, add small run test from tutorial, add coverage
parent
739090fd
Pipeline
#5438
passed with stage
Changes
5
Pipelines
1
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.gitignore
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67c620e2
example*
build
CMakeCache.txt
CMakeFiles
Makefile
...
...
.gitlab-ci.yml
View file @
67c620e2
...
...
@@ -7,7 +7,8 @@ before_script:
# tests have been done.
stages
:
-
build
# - coverage
-
test
-
coverage
# default build (without CUDA)
build-gcc-mpi-nocuda
:
...
...
.gitlab-ci/build/run_build.sh
0 → 100755
View file @
67c620e2
#!/bin/bash
ARCHITECTURE
=
$1
DEBUG
=
${
2
:-
no
}
.
/etc/profile.d/modules.sh
module use /afs/ipp/common/usr/modules.2014/@sys/modulefiles/GPU
module load cmake
echo
"building BioEM with ARCH=
$ARCHITECTURE
"
case
"
$ARCHITECTURE
"
in
intel-mpi
)
module load intel/15.0 impi/5.0.3 fftw/3.3.4 boost/intel/1.56
rm
-rf
build/
;
mkdir
build
cd
build
cmake ..
-DCMAKE_CXX_COMPILER
=
icpc
-DCMAKE_C_COMPILER
=
icc
make
VERBOSE
=
1
-j
2
;;
gcc-mpi
)
module load gcc/4.9 impi/5.0.3 fftw/gcc/3.3.4 boost/gcc/1.56
rm
-rf
build/
;
mkdir
build
cd
build
cmake ..
-DCMAKE_CXX_COMPILER
=
g++
-DCMAKE_C_COMPILER
=
gcc
-DCMAKE_BUILD_TYPE
=
Debug
-DCMAKE_CXX_FLAGS_DEBUG
=
'-g -Wall --coverage'
-DCMAKE_C_FLAGS_DEBUG
=
'-g -Wall --coverage'
make
VERBOSE
=
1
-j
2
;;
gcc-mpi-cuda
)
module load gcc/4.9 cuda/7.5 impi/5.0.3 fftw/gcc/3.3.4 boost/gcc/1.56
rm
-rf
build/
;
mkdir
build
cd
build
cmake ..
-DCMAKE_CXX_COMPILER
=
g++
-DCMAKE_C_COMPILER
=
gcc
-DUSE_CUDA
=
on
-DCUDA_CUDA_LIBRARY
=
$CUDA_HOME
/lib64/stubs/libcuda.so
make
VERBOSE
=
1
-j
2
;;
*
)
echo
"ARCHITECTURE
$ARCHITECTURE
not defined for build"
exit
1
;;
esac
module list
.gitlab-ci/test/run_coverage.sh
0 → 100755
View file @
67c620e2
#!/bin/bash
INPUT_DIR
=
$1
OUTPUT_DIR
=
$2
.
/etc/profile.d/modules.sh
module load gcc/4.9
mkdir
$OUTPUT_DIR
lcov
--no-checksum
--capture
--directory
$INPUT_DIR
--output-file
coverage.info
lcov
-r
coverage.info
*
/boost/
*
--output-file
coverage.info
lcov
-r
coverage.info /usr/
*
--output-file
coverage.info
lcov
-r
coverage.info /usr/include/
*
--output-file
coverage.info
lcov
-r
coverage.info
*
4.9.3
*
--output-file
coverage.info
genhtml coverage.info
--output-directory
$OUTPUT_DIR
.gitlab-ci/test/run_test.sh
0 → 100755
View file @
67c620e2
#!/bin/bash
#env
ARCH
=
$1
NUMPROCS
=
${
2
:-
4
}
NUMTHRDS
=
${
3
:-
2
}
.
/etc/profile.d/modules.sh
module load impi
export
OMP_NUM_THREADS
=
$NUMTHRDS
export
OMP_PLACES
=
cores
export
OMP_STACKSIZE
=
128M
cp
-r
Tutorial_BioEM test1
cd
test1
mpiexec
-n
$NUMPROCS
../build/bioEM
--Inputfile
Param_Input
--Modelfile
Model_Text
--Particlesfile
Text_Image_Form
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