Missing openmpi directory during compiling

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JMette
Posts: 5
Joined: Wed Oct 25, 2023 3:15 pm
Location: University of Bremen

Missing openmpi directory during compiling

#1 Unread post by JMette »

Hi all,

I have a question regarding the configuration of the upwelling test case with openmpi on our computing cluster. When I run in serial, everything works fine. Also, on my private computer, I'm able to run it with mpi in the default config. When I use openmpi, during compile time I get the following output:

Code: Select all

f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow -ffree-form -ffree-line-length-none mod_ice.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_stepping.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow -ffree-form -ffree-line-length-none round.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_eoscoef.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow lapack_mod.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow lubksb.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow ludcmp.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mp_routines.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow read_icepar.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow sqlq.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_param.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_iounits.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow nrutil.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_scalars.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow -ffree-form -ffree-line-length-none mod_sediment.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_behavior.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow shapiro.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow gasdev.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow -fno-strict-overflow ran_state.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow obs_k2z.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow ran1.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow exchange_2d.f90
cd /home/jmette/roms_project/roms_test/upwelling/Build_romsG; /usr/bin/mpif90 -c -frepack-arrays -fallow-argument-mismatch        -g -O0 -fbounds-check -fbacktrace -fcheck=all -finit-real=nan -ffpe-trap=invalid,zero,overflow mod_parallel.f90
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-15/openmpi’ [-Wmissing-include-dirs]
mod_parallel.f90:19: Error: Can't open included file 'mpif.h'
make: *** [ROMS/Modules/Module.mk:15: /home/jmette/roms_project/roms_test/upwelling/Build_romsG/mod_parallel.o] Error 1
make: *** Waiting for unfinished jobs....
For what I understand from that error, the build script cannot find the openmpi installation, right? I wait right now for more information on that from the person responsible for the computation cluster. But then would be my question:

How do I specify the custom path in the build script? Is it this block and if yes, how would a working example look like (I'm not so experienced with bash usage & co)?

Code: Select all

#--------------------------------------------------------------------------
# If applicable, use my specified library paths.
#--------------------------------------------------------------------------

 export USE_MY_LIBS=no            # use system default library paths
#export USE_MY_LIBS=yes           # use my customized library paths

MY_PATHS=${COMPILERS}/my_build_paths.sh

if [ "${USE_MY_LIBS}" == "yes" ]; then
  source ${MY_PATHS} ${MY_PATHS}
fi
Attached is also my build script, I'm very glad for any help!
Attachments
build_roms.sh
(16.58 KiB) Downloaded 4 times
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wilkin
Posts: 901
Joined: Mon Apr 28, 2003 5:44 pm
Location: Rutgers University
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Re: Missing openmpi directory during compiling

#2 Unread post by wilkin »

ROMS should be able to find what it needs in the system defaults, so your sysadmin build of MPI might be problematic.

If you need to customize the paths, it's best to do it in ./Compilers/my_build_paths.csh which will be used when (in build_roms.sh) you activate ...

Code: Select all

export USE_MY_LIBS=yes           # use my customized library paths
MY_PATHS=${COMPILERS}/my_build_paths.sh
John Wilkin: DMCS Rutgers University
71 Dudley Rd, New Brunswick, NJ 08901-8521, USA. ph: 609-630-0559 jwilkin@rutgers.edu
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