Comments (5)
jamal919
commented on June 30, 2024
Could it be related to the mismatch of gcc and ifort? Have you tried to use icc as the C compiler?
from schism.
zeekus
commented on June 30, 2024
I recompiled everything using gcc and gfortran and seem to get stopped at the same module. The 'hydro' module will not compile.
[root@ip-myip build]# module list
Currently Loaded Modulefiles:
- netcdf-fortran-4.5.4-gcc-4.8.5-damijzt 2) hdf5-1.12.2-gcc-4.8.5-cbshryq 3) openmpi-4.1.4-gcc-4.8.5-fiqiibx
[root@ip-myip build]# /usr/local/bin/cmake -D CMAKE_C_COMPILER=/usr/bin/gcc -D CMAKE_Fortran_COMPILER=/bin/gfortran -C ../cmake/SCHISM.local.build -C ../cmake/SCHISM.local.bora.gnu ../src/
loading initial cache file ../cmake/SCHISM.local.build
--
################ Begin SCHISM Configuration ################
-- In-source builds not allowed
-- The C compiler identification is GNU 4.8.5
-- The Fortran compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /bin/gfortran - skipped
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
--
### Your compiler is /bin/gfortran
--
### No CMAKE_BUILD_TYPE selected in command or cache, default to Release.
Alternatives are Debug and RelWithDebInfo
--
### Processing algorithmic switches and build options involving functionality for main project
-- Build definition tags set to _TVD-VL
--
### Configuring MPI Library
-- Found MPI_C: /root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/lib/libmpi.so (found version "3.1")
-- Found MPI_Fortran: /root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/lib/libmpi_usempi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- MPIVERSION = 2
--
### Configuring NetCDF
-- Found NetCDF: /usr/include;/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/include (found version "4.3.3.1") found components: C Fortran
-- FindNetCDF defines targets:
-- - NetCDF_VERSION [4.3.3.1]
-- - NetCDF_PARALLEL [FALSE]
-- - NetCDF_C_CONFIG_EXECUTABLE [/usr/bin/nc-config]
-- - NetCDF::NetCDF_C [SHARED] [Root: /usr] Lib: /usr/lib64/libnetcdf.so
-- - NetCDF_Fortran_CONFIG_EXECUTABLE [/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/bin/nf-config]
-- - NetCDF::NetCDF_Fortran [SHARED] [Root: /root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya] Lib: /root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/lib
/libnetcdff.so
--
### Assigning output directories for binaries (bin), modules (include) and libraries (lib)
--
### Adding enabled libraries to project
--
### Configuring ParMETIS
-- Using SCHISM's internal ParMETIS library.
CMake Deprecation Warning at ParMetis-4.0.3/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 2.8.12 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for getline
-- Looking for getline - found
-- checking for thread-local storage - found
-- PARMETIS_DIR: /home/centos/schism/src/ParMetis-4.0.3
-- PARMETIS_VER: ParMetis-4.0.3
-- hydro_extra_src=
-- Mod libraries:
-- Added Hydro
-- Added Core
--
### Configuring Driver
Using schism module libraries core;hydro
-- START: pschism_BORA_GNU:pschism_BORA_GNU
-- Executable name with this configuration will be pschism_BORA_GNU_TVD-VL
-- All defines:
--
### Configuring Utilities
-- In /Utility NetCDF_LIBS /usr/lib64/libnetcdf.so;/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/lib/libnetcdff.so
-- In /Utility NetCDF_LIBS /usr/lib64/libnetcdf.so;/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/lib/libnetcdff.so
-- In Utility/Gen_Hotstart
-- In Utility/Grid_Scripts
-- Configuring done
-- Generating done
-- Build files have been written to: /home/centos/schism/build
make pschism
[ 88%] Linking C static library ../../lib/libparmetis.a
cd /home/centos/schism/build/ParMetis-4.0.3/libparmetis && /usr/local/bin/cmake -P CMakeFiles/parmetis.dir/cmake_clean_target.cmake
cd /home/centos/schism/build/ParMetis-4.0.3/libparmetis && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/parmetis.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libparmetis.a CMakeFiles/parmetis.dir/akwayfm.c.o CMakeFiles/parmetis.dir/ametis.c.o CMakeFiles/parmetis.dir/balancemylink.c.o CMakeFiles/parmetis.dir/comm.c.o CMakeFiles/parmetis.dir/csrmatch.c.o CMakeFiles/parmetis.dir/ctrl.c.o CMakeFiles/parmetis.dir/debug.c.o CMakeFiles/parmetis.dir/diffutil.c.o CMakeFiles/parmetis.dir/frename.c.o CMakeFiles/parmetis.dir/gkmetis.c.o CMakeFiles/parmetis.dir/gkmpi.c.o CMakeFiles/parmetis.dir/graph.c.o CMakeFiles/parmetis.dir/initbalance.c.o CMakeFiles/parmetis.dir/initmsection.c.o CMakeFiles/parmetis.dir/initpart.c.o CMakeFiles/parmetis.dir/kmetis.c.o CMakeFiles/parmetis.dir/kwayrefine.c.o CMakeFiles/parmetis.dir/match.c.o CMakeFiles/parmetis.dir/mdiffusion.c.o CMakeFiles/parmetis.dir/mesh.c.o CMakeFiles/parmetis.dir/mmetis.c.o CMakeFiles/parmetis.dir/move.c.o CMakeFiles/parmetis.dir/msetup.c.o CMakeFiles/parmetis.dir/node_refine.c.o CMakeFiles/parmetis.dir/ometis.c.o CMakeFiles/parmetis.dir/pspases.c.o CMakeFiles/parmetis.dir/redomylink.c.o CMakeFiles/parmetis.dir/remap.c.o CMakeFiles/parmetis.dir/renumber.c.o CMakeFiles/parmetis.dir/rmetis.c.o CMakeFiles/parmetis.dir/selectq.c.o CMakeFiles/parmetis.dir/serial.c.o CMakeFiles/parmetis.dir/stat.c.o CMakeFiles/parmetis.dir/timer.c.o CMakeFiles/parmetis.dir/util.c.o CMakeFiles/parmetis.dir/wave.c.o CMakeFiles/parmetis.dir/weird.c.o CMakeFiles/parmetis.dir/wspace.c.o CMakeFiles/parmetis.dir/xyzpart.c.o
/usr/bin/ranlib ../../lib/libparmetis.a
make[3]: Leaving directory `/home/centos/schism/build'
[ 88%] Built target parmetis
make -f Hydro/CMakeFiles/hydro.dir/build.make Hydro/CMakeFiles/hydro.dir/depend
make[3]: Entering directory `/home/centos/schism/build'
cd /home/centos/schism/build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /home/centos/schism/src /home/centos/schism/src/Hydro /home/centos/schism/build /home/centos/schism/build/Hydro /home/centos/schism/build/Hydro/CMakeFiles/hydro.dir/DependInfo.cmake --color=
make[3]: Leaving directory `/home/centos/schism/build'
make -f Hydro/CMakeFiles/hydro.dir/build.make Hydro/CMakeFiles/hydro.dir/build
make[3]: Entering directory `/home/centos/schism/build'
[ 88%] Building Fortran object Hydro/CMakeFiles/hydro.dir/sflux_9c.F90.o
cd /home/centos/schism/build/Hydro && /bin/gfortran -DMPIVERSION=2 -DSCHISM -DTVD_VL -DUSE_HYDRO -DUSE_SCHISM -I/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/include -I/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/lib -I/usr/include -I/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/include -I/home/centos/schism/build/include -O2 -ffree-line-length-none -static-libgfortran -finit-local-zero -J../include -pthread -pthread -cpp -c /home/centos/schism/src/Hydro/sflux_9c.F90 -o CMakeFiles/hydro.dir/sflux_9c.F90.o
/usr/local/bin/cmake -E cmake_copy_f90_mod include/netcdf_io.mod Hydro/CMakeFiles/hydro.dir/netcdf_io.mod.stamp GNU
/usr/local/bin/cmake -E touch Hydro/CMakeFiles/hydro.dir/sflux_9c.F90.o.provides.build
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_init.F90.o
cd /home/centos/schism/build/Hydro && /bin/gfortran -DMPIVERSION=2 -DSCHISM -DTVD_VL -DUSE_HYDRO -DUSE_SCHISM -I/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/include -I/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/openmpi-4.1.4-fiqiibxuryj7kahjg7dhtuuirm4fjove/lib -I/usr/include -I/root/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/netcdf-fortran-4.5.4-damijztptvt6urkr4hdjthkspdsmpcya/include -I/home/centos/schism/build/include -O2 -ffree-line-length-none -static-libgfortran -finit-local-zero -J../include -pthread -pthread -cpp -c /home/centos/schism/src/Hydro/schism_init.F90 -o CMakeFiles/hydro.dir/schism_init.F90.o
/home/centos/schism/src/Hydro/schism_init.F90:503.24:
read(15,nml=SCHOUT)
1
Error: Symbol 'schout' at (1) must be a NAMELIST group name
/home/centos/schism/src/Hydro/schism_init.F90:527.27:
write(15,nml=SCHOUT)
1
Error: Symbol 'schout' at (1) must be a NAMELIST group name
make[3]: *** [Hydro/CMakeFiles/hydro.dir/schism_init.F90.o] Error 1
make[3]: Leaving directory `/home/centos/schism/build'
make[2]: *** [Hydro/CMakeFiles/hydro.dir/all] Error 2
make[2]: Leaving directory `/home/centos/schism/build'
make[1]: *** [Driver/CMakeFiles/pschism.dir/rule] Error 2
make[1]: Leaving directory `/home/centos/schism/build'
make: *** [pschism] Error 2
from schism.
zeekus
commented on June 30, 2024
I downloaded the lastet version of Schism and it appears to got to 100% but failed at the last step. What would cause this ?
/home/centos/schism/src/ParMetis-4.0.3/libparmetis/wave.c: In function ‘libparmetis__WavefrontDiffusion’:
/home/centos/schism/src/ParMetis-4.0.3/libparmetis/wave.c:253:1: warning: label ‘CleanUpAndExit’ defined but not used [-Wunused-label]
CleanUpAndExit:
^
[ 84%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/weird.c.o
[ 86%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/wspace.c.o
[ 86%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/xyzpart.c.o
[ 88%] Linking C static library ../../lib/libparmetis.a
[ 88%] Built target parmetis
[ 88%] Building Fortran object Hydro/CMakeFiles/hydro.dir/sflux_9c.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_init.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_step.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_finalize.F90.o
[ 92%] Building Fortran object Hydro/CMakeFiles/hydro.dir/bktrk_subs.F90.o
[ 92%] Building Fortran object Hydro/CMakeFiles/hydro.dir/grid_subs.F90.o
[ 94%] Building Fortran object Hydro/CMakeFiles/hydro.dir/lap.F90.o
[ 94%] Building Fortran object Hydro/CMakeFiles/hydro.dir/misc_subs.F90.o
[ 96%] Building Fortran object Hydro/CMakeFiles/hydro.dir/solver_subs.F90.o
[ 96%] Building Fortran object Hydro/CMakeFiles/hydro.dir/transport_TVD.F90.o
[ 98%] Building Fortran object Hydro/CMakeFiles/hydro.dir/transport_TVD_imp.F90.o
[ 98%] Linking Fortran static library ../lib/libhydro.a
[ 98%] Built target hydro
[100%] Building Fortran object Driver/CMakeFiles/pschism.dir/schism_driver.F90.o
[100%] Linking Fortran executable ../bin/pschism_BORA_GNU_TVD-VL
/bin/ld: cannot find -lgfortran
/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make[3]: *** [bin/pschism_BORA_GNU_TVD-VL] Error 1
make[2]: *** [Driver/CMakeFiles/pschism.dir/all] Error 2
make[1]: *** [Driver/CMakeFiles/pschism.dir/rule] Error 2
make: *** [pschism] Error 2
from schism.
josephzhang8
commented on June 30, 2024
Looks like you invoked gfortran somehow and its lib has issues.
from schism.
zeekus
commented on June 30, 2024
It appears the gcc libraries for gfortran where missing on your Centos7 box.
I had to install the 'libgfortran-static' library to get the 'make pschism' command to finish.
[centos@machine build]$ rpm -qal libgfortran-static
/usr/lib/gcc
/usr/lib/gcc/x86_64-redhat-linux
/usr/lib/gcc/x86_64-redhat-linux/4.8.2
/usr/lib/gcc/x86_64-redhat-linux/4.8.2/libgfortran.a
/usr/lib/gcc/x86_64-redhat-linux/4.8.5
Before:
/opt/schism/src/ParMetis-4.0.3/libparmetis/wave.c:253:1: warning: label ‘CleanUpAndExit’ defined but not used [-Wunused-label]
CleanUpAndExit:
^
[ 84%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/weird.c.o
[ 86%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/wspace.c.o
[ 86%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/xyzpart.c.o
[ 88%] Linking C static library ../../lib/libparmetis.a
[ 88%] Built target parmetis
[ 88%] Building Fortran object Hydro/CMakeFiles/hydro.dir/sflux_9c.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_init.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_step.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_finalize.F90.o
[ 92%] Building Fortran object Hydro/CMakeFiles/hydro.dir/bktrk_subs.F90.o
[ 92%] Building Fortran object Hydro/CMakeFiles/hydro.dir/grid_subs.F90.o
[ 94%] Building Fortran object Hydro/CMakeFiles/hydro.dir/lap.F90.o
[ 94%] Building Fortran object Hydro/CMakeFiles/hydro.dir/misc_subs.F90.o
[ 96%] Building Fortran object Hydro/CMakeFiles/hydro.dir/solver_subs.F90.o
[ 96%] Building Fortran object Hydro/CMakeFiles/hydro.dir/transport_TVD.F90.o
[ 98%] Building Fortran object Hydro/CMakeFiles/hydro.dir/transport_TVD_imp.F90.o
[ 98%] Linking Fortran static library ../lib/libhydro.a
[ 98%] Built target hydro
[100%] Building Fortran object Driver/CMakeFiles/pschism.dir/schism_driver.F90.o
[100%] Linking Fortran executable ../bin/pschism_BORA_GNU_TVD-VL
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make[3]: *** [bin/pschism_BORA_GNU_TVD-VL] Error 1
make[2]: *** [Driver/CMakeFiles/pschism.dir/all] Error 2
make[1]: *** [Driver/CMakeFiles/pschism.dir/rule] Error 2
make: *** [pschism] Error 2
After installing the missing library:
/opt/schism/src/ParMetis-4.0.3/libparmetis/wave.c: In function ‘libparmetis__WavefrontDiffusion’:
/opt/schism/src/ParMetis-4.0.3/libparmetis/wave.c:253:1: warning: label ‘CleanUpAndExit’ defined but not used [-Wunused-label]
CleanUpAndExit:
^
[ 84%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/weird.c.o
[ 86%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/wspace.c.o
[ 86%] Building C object ParMetis-4.0.3/libparmetis/CMakeFiles/parmetis.dir/xyzpart.c.o
[ 88%] Linking C static library ../../lib/libparmetis.a
[ 88%] Built target parmetis
[ 88%] Building Fortran object Hydro/CMakeFiles/hydro.dir/sflux_9c.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_init.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_step.F90.o
[ 90%] Building Fortran object Hydro/CMakeFiles/hydro.dir/schism_finalize.F90.o
[ 92%] Building Fortran object Hydro/CMakeFiles/hydro.dir/bktrk_subs.F90.o
[ 92%] Building Fortran object Hydro/CMakeFiles/hydro.dir/grid_subs.F90.o
[ 94%] Building Fortran object Hydro/CMakeFiles/hydro.dir/lap.F90.o
[ 94%] Building Fortran object Hydro/CMakeFiles/hydro.dir/misc_subs.F90.o
[ 96%] Building Fortran object Hydro/CMakeFiles/hydro.dir/solver_subs.F90.o
[ 96%] Building Fortran object Hydro/CMakeFiles/hydro.dir/transport_TVD.F90.o
[ 98%] Building Fortran object Hydro/CMakeFiles/hydro.dir/transport_TVD_imp.F90.o
[ 98%] Linking Fortran static library ../lib/libhydro.a
[ 98%] Built target hydro
[100%] Building Fortran object Driver/CMakeFiles/pschism.dir/schism_driver.F90.o
[100%] Linking Fortran executable ../bin/pschism_BORA_GNU_TVD-VL
[100%] Built target pschism
from schism.
Related Issues (20)
- Error copying Fortran module "include/schism_glbl.mod" HOT 23
- Incorrect Pi value in read_output10_xyz.f90 HOT 2
- Help SCHISM-WWM III HOT 1
- Update ugrid conventions HOT 13
- Help - pschism seems to not able to find the hdf5 libraries and netcdf-c libraries. HOT 3
- General Info: how to run Pschism on AWS pcluster with Spack HOT 1
- Format overflow in staout HOT 1
- Issue Running with Sflux generated from HAFS HOT 10
- No rule to make target 'pschism' / BLD_STANDALONE HOT 5
- Exit code is zero even when simulator fails HOT 3
- Compile GOTM 3.2.5 HOT 2
- Updating variable names in hotstart.nc HOT 6
- latest version in git wants deprecated NetCDF-Fotran build (with f90) HOT 7
- set_mask error during compilation of SCHISM-FABMv2-(ECOSMO) HOT 6
- FABM/SCHISM: UNFULFILLED DEPENDENCY: downwelling_photosynthetic_radiative_flux HOT 6
- Error when run a 2D model with tidal elevation and velocity ( 23: ABORT: STEP: wetted cross section length on open bnd <=0; boundary ndx= 1 , length= 0.000000000000000E+000) HOT 3
- Support for the Intel 2024+ compilers
- Julian Date Calculation Imprecision Leads to Issues with Time Indices Slicing in the sflux_air_1.0001.nc File HOT 3
- Missing inverse barometer effect? HOT 3
- Initial timesteps results for a hotstart run HOT 13
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from schism.