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schism-dev / schism

Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM)
http://ccrm.vims.edu/schismweb/
Apache License 2.0
78 stars 84 forks source link

Help - pschism seems to not able to find the hdf5 libraries and netcdf-c libraries. #115

Closed zeekus closed 7 months ago

zeekus commented 7 months ago

It appear pschism is not finding two libraries and dying: hdf5 and a netcdf

Is there a work around I might be able to use to tell cmake where these are ?

Here is my sbatch run.

[centos@ip-10-1-1-1 Test_ICM_ChesBay]$ cat pschism_job_beefy.27.err

Are you sure you want to clear all loaded modules!? [n] Currently Loaded Modulefiles:
  1) nghttp2/1.57.0-oneapi-2021.2.0-noyvzc
  2) zlib-ng/2.1.4-oneapi-2021.2.0-kxurjk
  3) openssl/3.1.3-oneapi-2021.2.0-ym4a5g
  4) curl/8.4.0-oneapi-2021.2.0-nvaxip
  5) ncurses/6.4-oneapi-2021.2.0-b6j3se
  6) cmake/3.27.7-oneapi-2021.2.0-ejhvyr
  7) libfabric/1.18.2-oneapi-2021.2.0-nfoyn4
  8) intel-mpi/2019.10.317-oneapi-2021.2.0-5uvyw3
  9) pkgconf/1.9.5-oneapi-2021.2.0-ownafr
 10) hdf5/1.14.3-oneapi-2021.2.0-ici6jg
 11) bzip2/1.0.8-oneapi-2021.2.0-2zpaqr
 12) lz4/1.9.4-oneapi-2021.2.0-om4aan
 13) snappy/1.1.10-oneapi-2021.2.0-4ne2lt
 14) zstd/1.5.5-oneapi-2021.2.0-gei5ma
 15) c-blosc/1.21.5-oneapi-2021.2.0-jhwqel
 16) libaec/1.0.6-oneapi-2021.2.0-knwa6h
 17) netcdf-c/4.9.2-oneapi-2021.2.0-g2kwkj
 18) netcdf-fortran/4.5.4-oneapi-2021.2.0-zr4nek
forrtl: severe (168): Program Exception - illegal instruction
Image              PC                Routine            Line        Source
pschism_AWS_SKYLA  000000000072DF5B  for__signal_handl     Unknown  Unknown
libpthread-2.17.s  00002B28CC5DE630  Unknown               Unknown  Unknown
libhdf5.so.310.3.  00002B28CD17F563  H5T__init_native_     Unknown  Unknown
libhdf5.so.310.3.  00002B28CD0E57D8  H5T_init              Unknown  Unknown
libhdf5.so.310.3.  00002B28CD1A3960  H5VL_init_phase2      Unknown  Unknown
libhdf5.so.310.3.  00002B28CCE35290  H5_init_library       Unknown  Unknown
libhdf5.so.310.3.  00002B28CCF04385  H5Eset_auto2          Unknown  Unknown
libnetcdf.so.19.2  00002B28C9B8010C  nc4_hdf5_initiali     Unknown  Unknown
libnetcdf.so.19.2  00002B28C9B8950C  NC_HDF5_initializ     Unknown  Unknown
libnetcdf.so.19.2  00002B28C9AEE808  nc_initialize         Unknown  Unknown
libnetcdf.so.19.2  00002B28C9AF3D7A  NC_open               Unknown  Unknown
libnetcdf.so.19.2  00002B28C9AF3A87  nc_open               Unknown  Unknown
libnetcdff.so.7.1  00002B28C9CF4442  nf_open_              Unknown  Unknown
libnetcdff.so.7.1  00002B28C9D37E39  netcdf_mp_nf90_op     Unknown  Unknown
pschism_AWS_SKYLA  000000000049D3E6  Unknown               Unknown  Unknown
pschism_AWS_SKYLA  0000000000410052  Unknown               Unknown  Unknown
pschism_AWS_SKYLA  000000000040FF92  Unknown               Unknown  Unknown
libc-2.17.so       00002B28CC80D555  __libc_start_main     Unknown  Unknown
pschism_AWS_SKYLA  000000000040FEA9  Unknown               Unknown  Unknown
srun: error: compute2-dy-slurmworkers-1: task 0: Exited with exit code 168

My CMakeCache.txt seems to reference them:

NETCDF:UNINITIALIZED=
NetCDF_C_DIR:UNINITIALIZED=/modeling/spack/opt/spack/linux-centos7-skylake_avx512/oneapi-2021.2.0/netcdf-c-4.9.2-g2kwkjh6nzll5z5cb3hlvehi3y36go7q
//Path to NetCDF Fortran library
NetCDF_FORTRAN_DIR:PATH=
NetCDF_INCLUDE_DIR:UNINITIALIZED=

Compiled binary like this: 

#!/usr/bin/bash
#filename:  /modeling/pschism/Test_ICM_ChesBay/compile_pschism_aws_intel-mpi.sh
#description: cmake file for compiling pschism with intel-mpi

#PSCHISM will not compile if the modules are not loaded first - check the modules
export MODULEPATH=$MODULEPATH:/modeling/spack/share/spack/modules/linux-centos7-skylake_avx512
module list -l  2> /var/tmp/modulelist

export module_load_file="/modeling/pschism/Test_ICM_ChesBay/load_modules_aws_intel.sh"
if ! grep -q "No Modulefiles Currently Loaded." /var/tmp/modulelist; then
    echo "Good:The module list is not empty"
else
    echo error: you will need to manually source the $module_load_file if it exists or manually load the desired modules.
    exit 1
fi

#load environment for mpi
source $(spack location -i intel-mpi@2019.10.317)/compilers_and_libraries_2020.4.317/linux/mpi/intel64/bin/mpivars.sh

#use spack set variables that are set in the ENV
#MPICC
#MPIFC
#MPIF77
#MPIF90
#MPICXX
#NETCDF_C_ROOT
#NETCDF_FORTRAN_ROOT
#HDF5_ROOT
#HDF5_PLUGIN_PATH
#INTEL_MPI_ROOT
#I_MPI_ROOT
#LIBFABRIC_ROOT
#LD_LIBRARY_PATH
#PATH
#CMAKE_PREFIX_PATH

#Set all the Variables
export I_MPI_PMI_LIBRARY="/opt/slurm/lib/libpmi2.so"
export FC="/modeling/spack/opt/spack/linux-centos7-skylake_avx512/gcc-9.2.0/intel-oneapi-compilers-2021.2.0-4pjd5dcymlvje6f7yohtwl7wsm6foy5k/compiler/2021.2.0/linux/bin/intel64/ifort"
export CC="/modeling/spack/opt/spack/linux-centos7-skylake_avx512/gcc-9.2.0/intel-oneapi-compilers-2021.2.0-4pjd5dcymlvje6f7yohtwl7wsm6foy5k/compiler/2021.2.0/linux/bin/intel64/icc"
export MPIIFORT="/modeling/spack/opt/spack/linux-centos7-skylake_avx512/oneapi-2021.2.0/intel-mpi-2019.10.317-5uvyw3tgr4lrkjko3ifa42bw3dhtbzyp/compilers_and_libraries_2020.4.317/linux/mpi/intel64/bin/mpiifort"
export CMAKE_Fortran_COMPILER=$MPIIFORT
export CMAKE_C_COMPILER=$MPICC
export CMAKE_CXX_COMPILER=$MPICXX
export NETCDF_C_ROOT=$NETCDF_C_ROOT
export NetCDF_C_DIR=$NETCDF_C_ROOT
export NETCDF_FORTRAN_ROOT=$NETCDF_FORTRAN_ROOT
export NetCDF_FORTRAN_DIR=$NETCDF_FORTRAN_ROOT
export NetCDF_LIBRARIES="$NETCDF_C_ROOT/lib"
export NetCDF_FORTRAN_LIBRARIES="$NETCDF_FORTRAN_ROOT/lib"
export HDF5_ROOT=$HDF5_ROOT
export CMAKE_BINARY=$(spack location -i cmake%oneapi@2021.2.0)/bin/cmake
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH
export PATH=$PATH
export local_build_for_cmake=/modeling/pschism/SCHISM.local.build
export custom_build_for_cmake=/modeling/pschism/SCHISM_local.cmake.bluefish.intel

#check to make sure the cmake files for the build are present
#Without these things may still compile but the application may not work as expected.
if [ -e "$local_build_for_cmake" ] && [ -e "$custom_build_for_cmake" ]; then
   echo "both the $local_build_for_cmake and the $custom_build_for_cmake exist"
else
   echo "ERROR either the $local_build_for_cmake or the $custom_build_for_cmake is missing error"
   exit 1
fi

#clean up the build folder
rm -fr /modeling/pschism/schism/src/build; mkdir /modeling/pschism/schism/src/build
#-D NetCDF_LIBRARIES=$NetCDF_LIBRARIES \

$CMAKE_BINARY -C $local_build_for_cmake -C $custom_build_for_cmake \
-D CMAKE_Fortran_COMPILER=$CMAKE_Fortran_COMPILER \
-D CMAKE_C_COMPILER=$CMAKE_C_COMPILER \
-D CMAKE_CXX_COMPILER=$CMAKE_C_COMPILER \
-D NetCDF_C_DIR=$NetCDF_C_DIR \
-D HDF5_DIR=$HDF5_ROOT \
-D NetCDF_INCLUDE_DIR=$NetCDF_INCLUDE_DIR \
-D NetCDF_FORTRAN_LIBRARIES=$NetCDF_FORTRAN_LIBRARIES \
-S /modeling/pschism/schism/src -B /modeling/pschism/schism/src/build

custom_build_for_cmake

set (SCHISM_EXE_BASENAME pschism_AWS_SKYLAKE CACHE STRING "Base name (modules and file extension to be added of the executable. If you want a machine name, add it here")

set(CMAKE_Fortran_COMPILER "$ENV{FC}" "Path to serial Fortran compiler")
set(CMAKE_C_COMPILER "ENV{$CC}" CACHE PATH "Path to serial Fortran compiler")
set(CMAKE_Fortran_COMPILER "$ENV{MPIF90}" CACHE PATH "Path to serial Fortran compiler")
set(CMAKE_C_COMPILER "$ENV{MPICC}"  CACHE PATH "Path to serial Fortran compiler")
set(HDF5_DIR "$ENV{HDF5_ROOT}" CACHE PATH "Path to HDF5 library")
set(NetCDF_C_DIR "$ENV{NETCDF_C_ROOT}" CACHE PATH "Path to NetCDF C")
set(NetCDF_C_LIBRARIES "$ENV{NETCDF_C_ROOT}/lib" CACHE PATH "Path to NetCDF C")
set(NetCDF_FORTRAN_DIR "$ENV{NETCDF_FORTRAN_ROOT}"  CACHE PATH "Path to NetCDF Fortran")
set(NetCDF_FORTRAN_LIBRARIES "$ENV{NETCDF_FORTRAN_ROOT}/lib" "Path to Fortran NetCDF Libaries")
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -init=zero -align array64byte" CACHE STRING "Fortran flags" FORCE)

make pschism

[centos@ip build]$ make -j8 pschism
[  2%] Building C object libmetis/CMakeFiles/metis.dir/__/GKlib/b64.c.o
/modeling/pschism/schism/src/Core/gen_version.py
/modeling/pschism/schism/src/Core
/modeling/pschism/schism/src/Core/_version
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[  4%] Building C object libmetis/CMakeFiles/metis.dir/__/GKlib/blas.c.o
[  4%] Building C object libmetis/CMakeFiles/metis.dir/__/GKlib/error.c.o
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[  6%] Building C object libmetis/CMakeFiles/metis.dir/__/GKlib/fs.c.o
SCHISM version not available, searching for src/schism_user_version.txt or default
Attempting to get version text manually from first line of
src/Core/schism_version_user.txt if file exists
5cd3b8e
 SCHISM version:  develop
 GIT commit       5cd3b8e
icc: command line warning #10006: ignoring unknown option '-cpp'
icc: command line warning #10006: ignoring unknown option '-cpp'
icc: command line warning #10006: ignoring unknown option '-cpp'
icc: command line warning #10006: ignoring unknown option '-cpp'
icc: command line warning #10006: ignoring unknown option '-cpp'
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icc: command line warning #10006: ignoring unknown option '-cpp'
/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(796): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel private(i, j, ncand, rsum, tsum, cand)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(800): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(839): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel private(i, j, ncand, rsum, tsum, cand)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(843): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1179): warning #3180: unrecognized OpenMP #pragma
    #pragma omp parallel if (n > 100)
    ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1185): warning #3180: unrecognized OpenMP #pragma
      #pragma omp single
      ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1192): warning #3180: unrecognized OpenMP #pragma
      #pragma omp for schedule(static)
      ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1331): warning #3180: unrecognized OpenMP #pragma
      #pragma omp parallel if (ptr[n] > OMPMINOPS)
      ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1333): warning #3180: unrecognized OpenMP #pragma
        #pragma omp for private(j,sum) schedule(static)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1359): warning #3180: unrecognized OpenMP #pragma
      #pragma omp parallel if (ptr[n] > OMPMINOPS)
      ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1361): warning #3180: unrecognized OpenMP #pragma
      #pragma omp for private(j,sum) schedule(static)
      ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1404): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1406): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j, maxtf) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1419): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1421): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j, maxtf) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1434): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1436): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1447): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1449): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1460): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1462): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1473): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1475): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1486): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1488): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1499): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1502): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for schedule(static,32)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1530): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (ncols > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1532): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1537): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1539): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1560): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (ncols > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1562): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for schedule(static) reduction(+:nnzcols)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1569): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1574): warning #3180: unrecognized OpenMP #pragma
        #pragma omp parallel if (rowptr[nrows] > OMPMINOPS)
        ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1576): warning #3180: unrecognized OpenMP #pragma
          #pragma omp for private(j) schedule(static)
          ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1633): warning #3180: unrecognized OpenMP #pragma
    #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static)
    ^

/modeling/pschism/schism/src/ParMetis-4.0.3/metis/GKlib/csr.c(1677): warning #3180: unrecognized OpenMP #pragma
    #pragma omp parallel for if (ptr[n] > OMPMINOPS) schedule(static)
    ^

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running it again

[centos@ip build]$ make -j8 pschism
/modeling/pschism/schism/src/Core/gen_version.py
/modeling/pschism/schism/src/Core
/modeling/pschism/schism/src/Core/_version
SCHISM version not available, searching for src/schism_user_version.txt or default
Attempting to get version text manually from first line of
src/Core/schism_version_user.txt if file exists
5cd3b8e
 SCHISM version:  develop
 GIT commit       5cd3b8e
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[100%] Built target hydro
[100%] Linking Fortran executable ../bin/pschism_AWS_SKYLAKE_ICM_OLDIO_PREC_EVAP_TVD-VL
[100%] Built target pschism
zeekus commented 7 months ago

I downloaded the latest source code, downloaded the newest data, recompiled, switched to the icm_Balg branch and re-ran things. I got the same result. 

git checkout -b remotes/origin/icm_Balg
Switched to a new branch 'remotes/origin/icm_Balg'

data source used https://columbia.vims.edu/schism/schism_verification_tests/Test_ICM_ChesBay

zeekus commented 7 months ago

This problem was resolved thanks. Not sure exactly what caused this. But, I rebuilt the stack and discovered a different issue.

zeekus commented 7 months ago

comment: resolved