diff --git "a/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" "b/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" index bcea9ef8777a53d57076c87c684533cb81a0970a..0eaa9e94f08baab5a7d11f125adb8a41712ece44 100644 --- "a/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" +++ "b/doc/ncl_nco_ncview/\343\200\212\345\237\272\344\272\216openEuler\347\232\204ncl_nco_ncview\350\275\257\344\273\266\347\247\273\346\244\215\346\214\207\345\215\227\343\200\213.md" @@ -58,7 +58,7 @@ | hdf-eos5 | 1.16 | | | hdf4 | 4.2.14 | | | hdf5 | 1.12.0 | | -| jasper | 1.900.1 | | +| jasper | 1.900.2 | | | libjpeg | v9b | | | libpng | 1.6.37 | | | Mesa | 3.1 | | @@ -303,11 +303,11 @@ cd proj-5.2.0 make all install #jasper -. wget -u https://www.ece.uvic.ca/~frodo/jasper/software/jasper_1.900.1.orig.tar.gz +. wget -u https://www.ece.uvic.ca/~frodo/jasper/software/jasper_1.900.2.orig.tar.gz cd $DEP_BUILD_DIR rm -rf jasper-1.900.2 -tar -xvf $DEP_DOWNLOAD_DIR/jasper_1.900.1.orig.tar.gz -cd jasper-1.900.1 +tar -xvf $DEP_DOWNLOAD_DIR/jasper_1.900.2.orig.tar.gz +cd jasper-1.900.2 ./configure --prefix=$1 make -j make install diff --git a/package/bisheng/2.3.0/install.sh b/package/bisheng/2.3.0/install.sh index d8fa5803ba5c76aba9b26bc1fd0cc7c9923f7ff2..442aacdbb3832eb8198cdb7180337e090fcf1617 100644 --- a/package/bisheng/2.3.0/install.sh +++ b/package/bisheng/2.3.0/install.sh @@ -1,3 +1,4 @@ #!/bin/bash -bisheng_ver='bisheng-compiler-2.3.0' +set -e +export bisheng_ver='bisheng-compiler-2.3.0' ../meta.sh $1 diff --git a/package/gdal/2.2.4/install.sh b/package/gdal/2.2.4/install.sh index b8b32c2e38bf3eef1f01ae1e48d606ec4f0d77d4..3e246ae081b92e6971f11df739118a822606cc77 100755 --- a/package/gdal/2.2.4/install.sh +++ b/package/gdal/2.2.4/install.sh @@ -3,13 +3,14 @@ set -x set -e . ${DOWNLOAD_TOOL} -u http://download.osgeo.org/gdal/2.2.4/gdal-2.2.4.tar.gz cd ${JARVIS_TMP} +rm -rf gdal-2.2.4 tar -xvf ${JARVIS_DOWNLOAD}/gdal-2.2.4.tar.gz cd gdal-2.2.4 ./configure --with-static-proj4=${PROJ_PATH} --prefix=$1 --with-png=${LIBPNG_PATH} --with-gif=internal --with-libtiff=internal \ --with-geotiff=internal --with-jpeg=${LIBJPEG_PATH} --with-libz=/usr/local \ --with-sqlite3=no --with-expat=no --with-curl=no --without-ld-shared \ - --with-hdf4=no --with-hdf5=no --with-pg=no --without-grib --disable-shared \ + --with-hdf4=no --with-hdf5=no --with-pg=no --without-grib --enable-shared \ --with-freexl=no --with-geos=no --with-openjpeg=no --with-mysql=no \ --with-ecw=no --with-fgdb=no --with-odbc=no --with-xml2=no --with-ogdi=no\ --with-pcraster=no --with-xerces=no diff --git a/package/hdf5/1.10.1/install.sh b/package/hdf5/1.10.1/install.sh index b2e8e3a3e26248b0e8636a9496a59f359170b88e..90aa738e6e8726e5f7481c1228a7c6bf0a6c94a2 100644 --- a/package/hdf5/1.10.1/install.sh +++ b/package/hdf5/1.10.1/install.sh @@ -9,5 +9,6 @@ tar -xvf ${JARVIS_DOWNLOAD}/hdf5-1.10.1.tar.gz cd hdf5-1.10.1 #CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort -Wno-incompatible-pointer-types-discards-qualifiers ./configure --prefix=$1 --enable-fortran --enable-static=yes --enable-parallel --enable-shared +sed -i '11835c wl="-Wl,"' libtool make -j make install diff --git a/package/hdf5/1.12.0/clang/install.sh b/package/hdf5/1.12.0/clang/install.sh index e2c320097621873abf925eb9911068039e139cc7..89603df35b099d7a12f846eb45ed8cfbd66c8f3e 100644 --- a/package/hdf5/1.12.0/clang/install.sh +++ b/package/hdf5/1.12.0/clang/install.sh @@ -8,7 +8,7 @@ cd ${JARVIS_TMP} rm -rf hdf5-${hdf5_version} tar -xvf ${JARVIS_DOWNLOAD}/hdf5-${hdf5_version}.tar.gz cd hdf5-${hdf5_version} -./configure --prefix=$1 --enable-fortran --enable-static=yes --enable-parallel --enable-shared CFLAGS="-O3 -fPIC -Wno-incompatible-pointer-types-discards-qualifiers -Wno-non-literal-null-conversion" FCFLAGS="-O3 -fPIC" LDFLAGS="-Wl,--build-id" +./configure --prefix=$1 --enable-fortran --enable-static=yes --with-zlib=/usr/lib --enable-parallel --enable-shared CFLAGS="-O3 -fPIC -Wno-incompatible-pointer-types-discards-qualifiers -Wno-non-literal-null-conversion" FCFLAGS="-O3 -fPIC" LDFLAGS="-Wl,--build-id" sed -i '11835c wl="-Wl,"' libtool make -j make install diff --git a/package/hdf5/1.12.0/install.sh b/package/hdf5/1.12.0/install.sh index 011e37e0da87e749576f577d2c2850ac0e60960f..f30c860476490bf0b988f887c75086f60789d6fd 100644 --- a/package/hdf5/1.12.0/install.sh +++ b/package/hdf5/1.12.0/install.sh @@ -8,6 +8,6 @@ cd ${JARVIS_TMP} rm -rf hdf5-${hdf5_version} tar -xvf ${JARVIS_DOWNLOAD}/hdf5-${hdf5_version}.tar.gz cd hdf5-${hdf5_version} -./configure --prefix=$1 --enable-fortran --enable-static=yes --enable-parallel --enable-shared +./configure --prefix=$1 --enable-fortran --enable-static=yes --enable-parallel --enable-shared --with-zlib=/usr/lib make -j make install diff --git a/package/jasper/1.900.2/install.sh b/package/jasper/1.900.2/install.sh index ade3fa523323afa97c01703ec5ac91788c4d336c..cdf5db72274536926be6357366b67116589b5e9c 100644 --- a/package/jasper/1.900.2/install.sh +++ b/package/jasper/1.900.2/install.sh @@ -1,13 +1,13 @@ -#download from https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.2.tar.gz +#download from https://www.ece.uvic.ca/~frodo/jasper/software/${jasper_ver}.tar.gz #!/bin/bash set -x set -e -. ${DOWNLOAD_TOOL} -u https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.2.tar.gz +jasper_ver="jasper-1.900.2" +. ${DOWNLOAD_TOOL} -u https://www.ece.uvic.ca/~frodo/jasper/software/${jasper_ver}.tar.gz cd ${JARVIS_TMP} -rm -rf jasper-1.900.2 -tar -xvf ${JARVIS_DOWNLOAD}/jasper-1.900.2.tar.gz -cd jasper-1.900.2 -#export CC=clang CXX=clang++ +rm -rf ${jasper_ver} +tar -xvf ${JARVIS_DOWNLOAD}/${jasper_ver}.tar.gz +cd ${jasper_ver} ./configure --prefix=$1 make -j make install diff --git a/package/libjpeg/v9b/install.sh b/package/libjpeg/v9b/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..ddfbf7d6c57819148053758501ca7c8b99edec19 --- /dev/null +++ b/package/libjpeg/v9b/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u http://www.ijg.org/files/jpegsrc.v9b.tar.gz +cd ${JARVIS_TMP} +rm -rf jpeg-9b +tar xvf ${JARVIS_DOWNLOAD}/jpegsrc.v9b.tar.gz +cd jpeg-9b +./configure --prefix=$1 --build=aarch64-unknown-linux-gnu +./configure --prefix=$1 CFLAGS="-fPIC" +make install diff --git a/package/udunits/2.2.28/install.sh b/package/udunits/2.2.28/install.sh index 655e44169da0f39acc7e6575476261f6e9b084bc..da426de3d09e9ba833717de304d506c69ff9e0a4 100644 --- a/package/udunits/2.2.28/install.sh +++ b/package/udunits/2.2.28/install.sh @@ -3,6 +3,7 @@ set -x set -e . ${DOWNLOAD_TOOL} -u https://artifacts.unidata.ucar.edu/repository/downloads-udunits/2.2.28/udunits-2.2.28.tar.gz cd ${JARVIS_TMP} +rm -rf udunits-2.2.28 tar xvf ${JARVIS_DOWNLOAD}/udunits-2.2.28.tar.gz cd udunits-2.2.28 ./configure --prefix=$1 diff --git a/package/zlib/1.2.11/clang/install.sh b/package/zlib/1.2.11/clang/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..8cad2b328afdc6295233feb6f21b42b07f0cac56 --- /dev/null +++ b/package/zlib/1.2.11/clang/install.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -x +set -e +zlib_ver='1.2.11' +. ${DOWNLOAD_TOOL} -u https://zlib.net/fossils/zlib-${zlib_ver}.tar.gz +cd ${JARVIS_TMP} +rm -rf zlib-${zlib_ver} +tar -xvf ${JARVIS_DOWNLOAD}/zlib-${zlib_ver}.tar.gz +cd zlib-${zlib_ver} +./configure --prefix=$1 FCFLAGS="-O3 -fPIC" +make -j +make install diff --git a/package/zlib/1.2.11/install.sh b/package/zlib/1.2.11/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..39c232ffcccb340aec5a1edf8e28f46a0a86dc1c --- /dev/null +++ b/package/zlib/1.2.11/install.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -x +set -e +zlib_ver='1.2.11' +. ${DOWNLOAD_TOOL} -u https://zlib.net/fossils/zlib-${zlib_ver}.tar.gz +cd ${JARVIS_TMP} +rm -rf zlib-${zlib_ver} +tar -xvf ${JARVIS_DOWNLOAD}/zlib-${zlib_ver}.tar.gz +cd zlib-${zlib_ver} +./configure --prefix=$1 +make -j +make install diff --git a/package/zlib/1.2.12/install.sh b/package/zlib/1.2.12/install.sh index 3b77899fc7d327d86c40fcbdc226e0481ea37130..9e3c1c6f6a040ef2d08b14d29973f696c6b598a6 100644 --- a/package/zlib/1.2.12/install.sh +++ b/package/zlib/1.2.12/install.sh @@ -2,7 +2,7 @@ set -x set -e zlib_ver='1.2.12' -. ${DOWNLOAD_TOOL} -u https://zlib.net/zlib-${zlib_ver}.tar.gz +. ${DOWNLOAD_TOOL} -u https://zlib.net/fossils/zlib-${zlib_ver}.tar.gz cd ${JARVIS_TMP} rm -rf zlib-${zlib_ver} tar -xvf ${JARVIS_DOWNLOAD}/zlib-${zlib_ver}.tar.gz diff --git a/templates/bcc-esm/bccesm.arm.cpu.config b/templates/bcc-esm/bccesm.arm.cpu.config index c0dd5f50645657ab634eab63bb8d578a777a4172..7e8b422bd03632c8d5a03e0467c05e87acafdabe 100644 --- a/templates/bcc-esm/bccesm.arm.cpu.config +++ b/templates/bcc-esm/bccesm.arm.cpu.config @@ -2,49 +2,58 @@ 11.11.11.11 [DOWNLOAD] -bcc-esm/4.0 http://forecast.bcccsm.ncc-cma.net/web/ +bcc-agcm/4.0 http://forecast.bcccsm.ncc-cma.net/web/?down_id=350 agcm.tar.gz [DEPENDENCY] set -x set -e -./jarvis -install kml/1.6.0/gcc any -./jarvis -install openblas/0.3.18 any ./jarvis -install bisheng/2.1.0 com module purge module use ./software/modulefiles -module load bisheng/2.1.0 -export CC=`which clang` CXX=`which clang++` FC=`which flang` +module load bisheng2/2.1.0 +export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` ./jarvis -install hmpi/1.1.1 bisheng -module load hmpi/1.1.1 +module load hmpi1/1.1.1 ./jarvis -bench mpi ./jarvis -install fftw/3.3.8 bisheng +./jarvis -bench mpi export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ./jarvis -install hdf5/1.10.1 clang+mpi ./jarvis -install pnetcdf/1.11.2 clang+mpi ./jarvis -install netcdf/4.7.0 clang+mpi -unzip ${JARVIS_DOWNLOAD}/esm.zip +tar -xvf BCC_ESM.tar [ENV] module purge -module use ./software/moduledeps -module use software/modulefiles -module load bisheng/2.1.0 -module load hmpi/1.1.1 -module load openblas/0.3.18 -module load kml-gcc/1.6.0 +module use /workspace/public/software/modules/ +module use software/moduledeps +module load compilers/bisheng/2.1.0/bisheng2.1.0 mpi/hmpi/1.1.1/bisheng2.1.0 libs/pnetcdf/1.12.1/bisheng2.1.0_hmpi1.1.1 libs/netcdf/netcdf_c_4.7.4_fortran_4.5.3/bisheng2.1.0_hmpi1.1.1 libs/fftw/3.3.8/bisheng2.1.0-hmpi1.1.1 libs/hdf5/1.12.0/bisheng2.1.0_hmpi1.1.1 +module load gcc7.3.0/openblas/0.3.18 export LIBS_DIR=/workspace/public/software/libs -export NETCDF_DIR=${NETCDF_PATH} -export PNETCDF_DIR=${PNETCDF_PATH} -export FFTW_DIR=${FFTW_PATH} -export MPI_DIR=${HMPI_PATH} +export NETCDF_DIR=${LIBS_DIR}/netcdf/netcdf_c_4.7.4_fortran_4.5.3/bisheng2.1.0_hmpi1.1.1 +export PNETCDF_DIR=${LIBS_DIR}/pnetcdf/1.12.1/bisheng2.1.0_hmpi1.1.1 +export FFTW_DIR=${LIBS_DIR}/fftw/3.3.8/bisheng2.1.0_hmpi1.1.1 +export MPI_DIR=/workspace/public/software/mpi/hmpi/1.1.1/bisheng2.1.0/ompi export USER_CC=mpicc export USER_FC=mpifort export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort +export CSMDATA=/workspace/home/BCC_ESM-T382/INIDATA +export DATA_PATH=$CSMDATA/data export MODEL_PATH=$JARVIS_ROOT/esm -export DATA_PATH=$JARVIS_ROOT/INIDATA/data -export CSMDATA=$JARVIS_ROOT/INIDATA export WORK_PATH=$MODEL_PATH/T382L70p25 -export KML_LIB=${KML_GCC_PATH}/lib + +export COMMON_PRECISE_OPT="-ffp-contract=off -mllvm -disable-sincos-opt -faarch64-pow-alt-precision=18 -mllvm -enable-alt-precision-math-functions -Hx,124,0xc00000 -Mflushz" +export LD_KML="-L${KML_LIB} -lkm_l9" +export ATM_PRECISE=$COMMON_PRECISE_OPT +export LND_PRECISE=$COMMON_PRECISE_OPT +export ICE_PRECISE=$COMMON_PRECISE_OPT +export OCN_PRECISE=$COMMON_PRECISE_OPT +export CPL_PRECISE=$COMMON_PRECISE_OPT +chmod +x -R $MODEL_PATH/tools +chmod +x -R $WORK_PATH/*.csh +chmod +x -R $MODEL_PATH/models [APP] app_name = BCCESM @@ -53,11 +62,11 @@ binary_dir = case_dir = $WORK_PATH [BUILD] -rm -rf output/atm/atm -rm -rf output/lnd/lnd -rm -rf output/ocn/ocn -rm -rf output/cpl/cpl -rm -rf output/ice/ice +#rm -rf output/atm/atm +#rm -rf output/lnd/lnd +#rm -rf output/ocn/ocn +#rm -rf output/cpl/cpl +#rm -rf output/ice/ice csh -f build.csh 1 [CLEAN] @@ -66,14 +75,13 @@ rm -rf OBJ [RUN] #run = ./build.csh 2 2>&1 | tee run.log run = ./build.csh 2 -binary = +binary = nodes = 1 [BATCH] #! /bin/bash - time1=$(date "+%Y-%m-%d"); -perfdir="perf-data/${time1}" +perfdir="perf-data/${time1}-28n-AJ-IJ-CPL8t-2day-8min" mkdir $perfdir cp output/atm/atm.log.* $perfdir/atm.log cp output/atm/timing.0 $perfdir/timing.atm.log @@ -83,23 +91,23 @@ cp output/lnd/lnd.log.* $perfdir/lnd.log cp output/lnd/timing.0 $perfdir/timing.lnd.log cp output/ocn/ocn.log.* $perfdir/ocn.log echo "All of the data has archived under $perfdir" - -# PRECT_GPCP(gpcp_vars) SST_HADISST TS_NCEP +PRECT_GPCP(gpcp_vars) SST_HADISST TS_NCEP exit 0 outputdir="job10-12M" -export MSS_testpath=/share/output/atm -export WKDIR=$JARVIS_ROOT/diag-ncl/$outputdir/ + +export MSS_testpath=/share/esm10/T382L70p25/output10-121n-8cpl/atm +#export WKDIR=$JARVIS_ROOT/diag-ncl/cn-test/$outputdir/ image_dir=$WKDIR/${outputdir}-obs export test_prefix=$outputdir cd $MSS_testpath echo "COMPUTE TEST CASE CLIMATOLOGY..." cur_var="" for n in {1..12}; do - if [ $n -lt 10 ]; then - cur_var="$cur_var historical.cam2.h0.2001-0$n.nc" - else - cur_var="$cur_var historical.cam2.h0.2001-$n.nc" - fi +if [ $n -lt 10 ]; then +cur_var="$cur_var historical.cam2.h0.2001-0$n.nc" +else +cur_var="$cur_var historical.cam2.h0.2001-$n.nc" +fi done echo "handing $cur_var" ncea -4 -O $cur_var ${test_prefix}_ANN_climo.nc @@ -112,4 +120,4 @@ cd $outputdir cp $image_dir/set5_6/set5_ANN_TS_NCEP_obsc.gif ./ cp $image_dir/set5_6/set5_ANN_SST_HADISST_obsc.gif ./ cp $image_dir/set5_6/set5_ANN_PRECT_GPCP_obsc.gif ./ -cp $image_dir/set7/set7_ANN_ICEFRAC_HADISST_NP_obsc.gif ./ \ No newline at end of file +cp $image_dir/set7/set7_ANN_ICEFRAC_HADISST_NP_obsc.gif ./ diff --git a/templates/bcc-esm/build.csh b/templates/bcc-esm/build.csh index 0f5e02d6fd8fe4a7fc8ccf74194d4082378c7aa2..46b83cab8bd133798a73e7a3d661a9269ba1b9e6 100644 --- a/templates/bcc-esm/build.csh +++ b/templates/bcc-esm/build.csh @@ -6,7 +6,6 @@ setenv MPI_ROOT ${MPI_DIR} limit datasize unlimited setenv XLSMPOPTS stack=860000000 -setenv OMP_STACKSIZE 3G setenv Atmosphere_Model CAM3 setenv System_Time_Type day # month/day @@ -158,6 +157,7 @@ if ( $argv[1] == 1 ) then $SCRIPTS/esmf.setup.csh >>& esmf.log.$LID || exit 1 endif + echo ------------------------------------------------------------------------- echo h. Execute component setup.csh scripts, build models echo ------------------------------------------------------------------------- @@ -202,13 +202,15 @@ end if ( $argv[1] == 2 ) then cd $EXEROOT - rm -rf atm/historical.cam2* atm/atm.log.* cpl/cpl.log.* esmf/esmf.log.* ice/ice.log.* lnd/lnd.log.* - rm -rf ocn/ocn.log.* esm_* esm_err_* + rm -rf atm/historical.cam2* atm/atm.log.* cpl/cpl.log.* ice/ice.log.* lnd/lnd.log.* ocn/ocn.log.* + rm -rf atm/timing.* atm/spmdstats.* + rm -rf esm_* echo ------------------------------------------------------------------------- echo j. Run the model, execute models simultaneously allocating CPUs echo ------------------------------------------------------------------------- echo "`date` -- CSM EXECUTION BEGINS HERE" setenv I_MPI_COMPATIBILITY 4 + setenv OMP_STACKSIZE 3G setenv KMP_AFFINITY compact echo "`date` -- CSM JOB SUBMIT HAS FINISHED" chmod +x run.sh diff --git a/templates/bcc-esm/run.sh b/templates/bcc-esm/run.sh index 6aa258db1c0e36f75b63a80e3eb12e43750c56a4..abbf99cb2eca47b0a4b2cd4730349cd2c1490179 100644 --- a/templates/bcc-esm/run.sh +++ b/templates/bcc-esm/run.sh @@ -1,7 +1,7 @@ #!/bin/bash -#DSUB -n esm-29n +#DSUB -n esm-28n #DSUB --job_type cosched -#DSUB -N 29 +#DSUB -N 28 #DSUB -R "cpu=128;mem=256000" #DSUB -A root.default #DSUB -q root.default @@ -28,10 +28,10 @@ ntask=`cat ${CCSCHEDULER_ALLOC_FILE} | sort | awk -v fff="$HOSTFILE" '{} total_task+=a[2] } }END{print total_task}'` -head -n 28 $HOSTFILE > $tmpfs -sed -i 's/128/96/' $tmpfs +head -n 27 $HOSTFILE > $tmpfs +sed -i 's/128/126/' $tmpfs tail -n 1 $HOSTFILE >> $tmpfs -sed -i 's/128/24/' $tmpfs +sed -i 's/128/128/' $tmpfs mv $tmpfs $HOSTFILE echo "openmpi hostfile $HOSTFILE generated:" echo "-----------------------" @@ -39,7 +39,7 @@ cat $HOSTFILE echo "-----------------------" echo "Total tasks is $ntask" echo "mpirun -hostfile $HOSTFILE -n $ntask " -sed -i "15c layout =20,10," ocn/input.nml +sed -i "15c layout =40,20," ocn/input.nml #generate run_roce.sh cat <<\EOF > run_roce.sh #!/bin/bash @@ -47,7 +47,7 @@ rank=$OMPI_COMM_WORLD_RANK idx=$(expr $rank % 32 / 8) # atm lnd ice ocn cpl -NTASKS=( 2304 96 96 200 16 ) +NTASKS=( 2304 116 182 800 8 ) NTHRDS=( 1 1 1 1 1 ) lnd_proc=`expr ${NTASKS[0]} + ${NTASKS[1]}` @@ -81,6 +81,6 @@ fi EOF chmod +x run_roce.sh date -mpirun --allow-run-as-root --mca plm_rsh_agent /opt/batch/agent/tools/dstart -mca btl ^vader,tcp,openib,uct -mca coll ^ucx -x UCX_BUILTIN_ALLREDUCE_ALGORITHM=6 -x UCX_BUILTIN_ALLTOALLV_ALGORITHM=1 -hostfile $HOSTFILE -np 2712 -x LD_LIBRARY_PATH -x PATH -x OMP_WAIT_POLICY=ACTIVE --bind-to socket run_roce.sh +mpirun --allow-run-as-root --mca plm_rsh_agent /opt/batch/agent/tools/dstart --mca pml ucx -mca btl ^vader,tcp,openib,uct -x UCX_NET_DEVICES=mlx5_0:1 -x UCX_BUILTIN_ALLREDUCE_ALGORITHM=6 -x UCX_BUILTIN_ALLTOALLV_ALGORITHM=1 -hostfile $HOSTFILE -np 3410 -x LD_LIBRARY_PATH -x PATH -x OMP_WAIT_POLICY=ACTIVE --bind-to core run_roce.sh #/share/fang/osu_init date exit 0 diff --git a/templates/ncl/6.6.2/data.NCL.arm.cpu.config b/templates/ncl/6.6.2/data.NCL.arm.cpu.config index 151aa61e9eba09a9ee9dad3f58b25c43c53e81d3..5c40ba84f72640e91425683f9396e649c77991fd 100644 --- a/templates/ncl/6.6.2/data.NCL.arm.cpu.config +++ b/templates/ncl/6.6.2/data.NCL.arm.cpu.config @@ -34,7 +34,7 @@ module load pnetcdf/1.12.1 sed -i '9c ./configure --prefix=$1 --enable-netcdf-4 --disable-shared' package/szip/2.1.1/install.sh -sed -i '11c CC=`which mpicc` FC=`which mpifort` ./configure --with-zlib=/usr/lib --prefix=$1 --enable-static=yes --enable-parallel --enable-shared --with-szlib=${JARVIS_LIBS}/bisheng2.3.0/szip/2.1.1/lib' package/hdf5/1.10.4/install.sh +sed -i '11c CC=`which mpicc` FC=`which mpifort` ./configure --with-zlib=/usr/lib --prefix=$1 --enable-static=yes --enable-parallel --enable-shared --with-szlib=${JARVIS_LIBS}/bisheng2.3.0/szip/2.1.1/lib' package/hdf5/1.12.0/install.sh sed -i 's/# sed/sed/g' package/hdf5/1.12.0/install.sh ./jarvis -install hdf5/1.12.0 bisheng @@ -50,11 +50,11 @@ ln -s -f ${NETCDF_PATH}/lib/libnetcdf.so.18 ${NETCDF_PATH}/lib/libnetcdf.so.15 ./jarvis -install hdf4/4.2.13 bisheng -module load hdf5/1.12.0 +module load hdf4/4.2.13 ln -s -f ${HDF5_PATH}/lib/libhdf5_hl.so.200.0.0 ${HDF5_PATH}/lib/libhdf5_hl.so.100 ln -s -f ${HDF5_PATH}/lib/libhdf5.so.200.0.0 ${HDF5_PATH}/lib/libhdf5.so.103 -./jarvis -install jasper/1.900.1 bisheng -module load jasper/1.900.1 +./jarvis -install jasper/1.900.2 bisheng +module load jasper/1.900.2 ln -s -f ${JASPER_PATH}/lib/libjasper.so.1.0.0 ${JASPER_PATH}/lib/libjasper.so.4 ./jarvis -install proj/5.2.0 bisheng @@ -71,6 +71,7 @@ export FC=`which flang` ./jarvis -install udunits/2.2.28 bisheng ./jarvis -install gsl/2.6 bisheng module load gsl/2.6 +module load udunits/2.2.28 ln -s -f ${GSL_PATH}/lib/libgsl.so.25.0.0 ${GSL_PATH}/lib/libgsl.so.23 ./jarvis -install openblas/0.3.18 bisheng module load openblas/0.3.18 @@ -87,10 +88,9 @@ module load hmpi/1.2.0 module load libjpeg/v9b module load hdf5/1.12.0 module load netcdf/4.7.4 -module load hdf4-clang/4.2.15 -module load hdf5/1.10.4 +module load hdf4/4.2.13 module load gsl/2.6 -module load jasper/1.900.1 +module load jasper/1.900.2 module load proj/5.2.0 module load gdal/2.2.4 module load udunits/2.2.28 @@ -114,11 +114,11 @@ rm -rf ncl_ncarg_6.6.2 mkdir ncl_ncarg_6.6.2 cd ncl_ncarg_6.6.2 rpm2cpio ${JARVIS_DOWNLOAD}/ncl-6.6.2-12.el8.aarch64.rpm | cpio -div -cp -r usr/* ${JARVIS_LIBS}/bisheng2.3.0/ncl +cp -r usr ${JARVIS_LIBS}/bisheng2.3.0/ncl export PATH=$PATH:${JARVIS_LIBS}/bisheng2.3.0/ncl/bin export NCARG_ROOT=${binary_dir} [RUN] -run = export PATH=$PATH:${JARVIS_LIBS}/bisheng2.3.0/ncl/bin && export NCARG_ROOT=${JARVIS_LIBS}/bisheng2.3.0/ncl && export NCARG_COLORMAPS=$NCARG_ROOT/lib64/ncarg/colormaps && ncl -Q +run = export PATH=$PATH:${JARVIS_LIBS}/bisheng2.3.0/ncl/bin && export NCARG_ROOT=${JARVIS_LIBS}/bisheng2.3.0/ncl && ncl -V binary = nodes = 1 diff --git a/templates/ncl/6.6.2/data.NCL.x86.cpu.config b/templates/ncl/6.6.2/data.NCL.x86.cpu.config index d172fcfe0a694f5b1cfe8dde92503e5a4034c6c4..09540bb1a1ccf7c71a97aa381de11fe93e25af54 100644 --- a/templates/ncl/6.6.2/data.NCL.x86.cpu.config +++ b/templates/ncl/6.6.2/data.NCL.x86.cpu.config @@ -144,7 +144,7 @@ sed -i '/#define ManRoot/a \ #define LibPath ${JARVIS_LIBS}/gcc10.3.0/ncl/lib \ #define IncPath ${JARVIS_LIBS}/gcc10.3.0/ncl/include \ #define ManPath ${JARVIS_LIBS}/gcc10.3.0/ncl/man \ -#define LibSearch -L/usr/lib64 -L/usr/local/lib -ltirpc -L${LIBJPEG_PATH}/lib -L${LIBPNG_PATH}/lib -L${JARVIS_LIBS}/gcc10.3.0/jasper/1.900.1/lib -L${JARVIS_LIBS}/gcc10.3.0/szip/2.1.1/lib -L${JARVIS_LIBS}/gcc10.3.0/cairo/1.16.0/lib -L${JARVIS_LIBS}/gcc10.3.0/pixman/0.38.0/lib -L${JARVIS_MPI}/openmpi4.1.2-gcc10.3.0/4.1.2/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf5/1.10.4/lib -L${JARVIS_LIBS}/gcc10.3.0/gsl/2.6/lib -L${JARVIS_LIBS}/gcc10.3.0/netcdf/4.7.4/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf4/4.2.15/lib -L${JARVIS_LIBS}/gcc10.3.0/cairo/1.16.0/lib -L${JARVIS_LIBS}/gcc10.3.0/udunits/2.2.28/lib -L${JARVIS_LIBS}/gcc10.3.0/g2clib/1.6.0/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf-eos2/2.20/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf-eos5/1.16/lib\ +#define LibSearch -L/usr/lib64 -L/usr/local/lib -ltirpc -L${LIBJPEG_PATH}/lib -L${LIBPNG_PATH}/lib -L${JARVIS_LIBS}/gcc10.3.0/jasper/1.900.2/lib -L${JARVIS_LIBS}/gcc10.3.0/szip/2.1.1/lib -L${JARVIS_LIBS}/gcc10.3.0/cairo/1.16.0/lib -L${JARVIS_LIBS}/gcc10.3.0/pixman/0.38.0/lib -L${JARVIS_MPI}/openmpi4.1.2-gcc10.3.0/4.1.2/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf5/1.10.4/lib -L${JARVIS_LIBS}/gcc10.3.0/gsl/2.6/lib -L${JARVIS_LIBS}/gcc10.3.0/netcdf/4.7.4/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf4/4.2.15/lib -L${JARVIS_LIBS}/gcc10.3.0/cairo/1.16.0/lib -L${JARVIS_LIBS}/gcc10.3.0/udunits/2.2.28/lib -L${JARVIS_LIBS}/gcc10.3.0/g2clib/1.6.0/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf-eos2/2.20/lib -L${JARVIS_LIBS}/gcc10.3.0/hdf-eos5/1.16/lib\ #define IncSearch -I/usr/local/include -I${LIBPNG_PATH}/include -I${JARVIS_MPI}/openmpi4.1.2-gcc10.3.0/4.1.2/include -I${JARVIS_LIBS}/gcc10.3.0/hdf5/1.10.4/include -I${JARVIS_LIBS}/gcc10.3.0/gsl/2.6/include -I${JARVIS_LIBS}/gcc10.3.0/netcdf/4.7.4/include -I${JARVIS_LIBS}/gcc10.3.0/hdf4/4.2.15/include -I${JARVIS_LIBS}/gcc10.3.0/cairo/1.16.0/include -I${JARVIS_LIBS}/gcc10.3.0/freetype/2.5.1/include -I${JARVIS_LIBS}/gcc10.3.0/udunits/2.2.28/include -I${JARVIS_LIBS}/gcc10.3.0/g2clib/1.6.0/include -I${JARVIS_LIBS}/gcc10.3.0/hdf-eos2/2.20/include -I${JARVIS_LIBS}/gcc10.3.0/hdf-eos5/1.16/include\ #define XdrLibrary -ltirpc' ./Site diff --git a/templates/nco/5.1.4/data.NCO.arm.cpu.config b/templates/nco/5.1.4/data.NCO.arm.cpu.config index 8d52a9a100e22cf11e2690590de6bb1dd04bcfaa..d3bd3e166ca3075c1a3464ec6832d5be5119a08e 100644 --- a/templates/nco/5.1.4/data.NCO.arm.cpu.config +++ b/templates/nco/5.1.4/data.NCO.arm.cpu.config @@ -18,9 +18,11 @@ module load libjpeg/v9b module load hmpi/1.2.0 -sed -i '5c hdf5_version="${hdf5_big_version}.0"' package/hdf5/1.12.0/clang/install.sh -CC=`which mpicc` ./jarvis -install hdf5/1.12.0/clang bisheng -module load hdf5-clang/1.12.0 +sed -i '5c hdf5_version="${hdf5_big_version}.0"' package/hdf5/1.12.0/install.sh +CC=`which mpicc` ./jarvis -install hdf5/1.12.0 bisheng +module load hdf5/1.12.0 +./jarvis -install hdf4/4.2.13/ bisheng +module load hdf4/4.2.13 sed -i '21c ./configure --prefix=$1 ${build_type} --enable-shared --enable-netcdf-4 --disable-dap --with-pic --disable-doxygen --enable-static --disable-pnetcdf --enable-largefile CPPFLAGS="-O3 -I${HMPI_PATH}/include -I${HDF5_DIR}/include -I${PNETCDF_DIR}/include" LDFLAGS="-L${HDF5_DIR}/lib -L${PNETCDF_DIR}/lib -Wl,-rpath=${HDF5_DIR}/lib -Wl,-rpath=${PNETCDF_DIR}/lib" CFLAGS="-O3 -L${HDF5_DIR}/lib -L${PNETCDF_DIR}/lib -I${HDF5_DIR}/include -I${PNETCDF_DIR}/include"' package/netcdf/4.7.4/install.sh ./jarvis -install netcdf/4.7.4 bisheng module load netcdf/4.7.4 @@ -36,12 +38,16 @@ module use ./software/modulefiles module load bisheng/2.3.0 module load hmpi/1.2.0 +module load hdf5/1.12.0 +module load hdf4/4.2.13 module load netcdf/4.7.4 module load gsl/2.6 module load antlr/2.7.7 module load udunits/2.2.28 export CC=`which clang` +export CXX=`which clang++` +export FC=`which flang` diff --git a/templates/ncview/2.1.7/data.ncview.arm.cpu.config b/templates/ncview/2.1.7/data.ncview.arm.cpu.config index 6e4653df79b1d207583fd627b2c51eea60e8fe05..e5abeb9b73e81cbd1286e480a99f30eb61bf9741 100644 --- a/templates/ncview/2.1.7/data.ncview.arm.cpu.config +++ b/templates/ncview/2.1.7/data.ncview.arm.cpu.config @@ -12,7 +12,9 @@ export CC=clang CXX=clang++ FC=flang module load hmpi/1.1.1 export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort ./jarvis -install hdf5/1.10.1 clang+mpi +module add hdf5/1.10.1 ./jarvis -install pnetcdf/1.11.2 bisheng+mpi +module load pnetcdf/1.11.2 ./jarvis -install netcdf/4.7.0 clang+mpi ./jarvis -install udunits/2.2.28 clang+mpi @@ -21,18 +23,22 @@ module purge module use ${JARVIS_ROOT}/software/modulefiles module add bisheng/2.1.0 module add hmpi/1.1.1 +module add hdf5/1.10.1 +module add pnetcdf/1.11.2 +module add netcdf/4.7.0 +module add udunits/2.2.28 export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort [APP] app_name = ncview build_dir = ${JARVIS_ROOT} binary_dir = -case_dir = +case_dir = ${JARVIS_LIBS}/bisheng2.1.0/hmpi1.1.1/ncview/2.1.7/bin [BUILD] ./jarvis -install ncview/2.1.7 clang+mpi [RUN] -run = +run = ./ncview binary = -node = 1 +nodes = 1 diff --git a/templates/ncview/2.1.7/data.ncview.x86.cpu.config b/templates/ncview/2.1.7/data.ncview.x86.cpu.config index 903579a8ee206923bc1dd37f9310ef6c3cc0f073..b967a0548f4a82f1a572773edfe1b25fd02cce08 100644 --- a/templates/ncview/2.1.7/data.ncview.x86.cpu.config +++ b/templates/ncview/2.1.7/data.ncview.x86.cpu.config @@ -39,7 +39,8 @@ case_dir = ./jarvis -install netcdf/4.7.4 gcc sed -i '13c NETCDF_DIR=${1%/*/*}/netcdf/4.7.4' package/ncview/2.1.7/install.sh ./jarvis -install ncview/2.1.7 gcc + [RUN] run = binary = -node = 1 +nodes = 1