Hello DG, Joel, > /share/apps/openmpi-1.6.5/include/mpi.h is readable. I think the > problem is with Cactus not recognizing the options for some reason. That would have been my guess. Yet in
configs/sim/bindings/Configuration/Capabilities/make.MPI.defn it has: INC_DIRS += $(MPI_INC_DIRS) MPI_INC_DIRS = /share/apps/openmpi-1.6.5/include and even if HDF5 itself did not bring in MPI (maybe it would not even though MPI shows up in its make.HDF5.deps file ...) IOHDF5Util (whose source file gave you the error) does explicitly depend on MPI through its configuration.ccl file which includes: OPTIONAL MPI which has me quite confused. Hence the request for the export VERBOSE=yes make fixedmhd output since that one will output the exact compiler line that Cactus executes and will tell us exactly if the proper -I option was included. Joel's solution (setting CC and CXX to mpicc and mpicxx) will also work on the cluster where you have a pre-compiled OpenMPI but won't work when you do actually compile OpenMPI inside of Cactus since mpicc naturally does not exist at the time it would be needed to compile OpenMPI itself. Yours, Roland > > > On Mar 21, 2018, at 9:52 AM, Roland Haas <[email protected]> wrote: > > > > Hello DG, > > > > hmm that all look fine to me. From the content of > > configs/sim/bindings/Configuration/Capabilities/make.MPI.defn it > > is using a system installed MPI (openmpi-1.6.5 in /share/apps) > > which makes sense given that you pass > > MPI_DIR=/share/apps/openmpi-1.6.5 in your config-info (which is > > basically a copy of your option list). So MPI_DIR=BUILD was not > > used in the end (through an oversight or something else I guess). > > > > Since you are passing an explicit > > > > MPI_INC_DIRS=/share/apps/openmpi-1.6.5/include > > > > I would definitely myself try and see if indeed there is a file > > > > /share/apps/openmpi-1.6.5/include/mpi.h > > > > and that this file is readable to your user account (eg does > > less /share/apps/openmpi-1.6.5/include/mpi.h work?). > > > > This is just in case /share/apps/openmpi-1.6.5 was eg retired by the > > sysadmins. > > > > Yours, > > Roland > > > >> Hello, > >> > >> Please see below. I’m using UH’s Maxwell cluster and don’t use > >> simfactory. > >> > >> Thanks, > >> > >> -DG > >> > >>> On Mar 20, 2018, at 11:47 AM, Roland Haas > >>> <[email protected]> wrote: > >>> > >>> Hello DG, > >>> > >>> it could be that something failed while MPI was compiled. Would > >>> you mind attaching the following files from inside of your Cactus > >>> tree, please? > >>> > >>> configs/sim/bindings/Configuration/Capabilities/make.MPI.defn > >> > >> INC_DIRS += $(MPI_INC_DIRS) > >> INC_DIRS_F += $(MPI_LIB_DIRS) > >> MPI_BUILD = > >> MPI_INSTALL_DIR = > >> HWLOC_DIR = > >> CCTK_MPI = 1 > >> MPI_DIR = /share/apps/openmpi-1.6.5 > >> MPI_INC_DIRS = /share/apps/openmpi-1.6.5/include > >> MPI_LIB_DIRS = /share/apps/openmpi-1.6.5/lib > >> MPI_LIBS = mpi mpi_cxx open-rte open-pal dl nsl util > >> HAVE_CAPABILITY_MPI = 1 > >> > >>> configs/sim/bindings/Configuration/Capabilities/make.HDF5.defn > >> > >> include > >> /home/dgarriso/Cactus/configs/fixedmhd/bindings/Configuration/Capabilities/make.MPI.defn > >> include > >> /home/dgarriso/Cactus/configs/fixedmhd/bindings/Configuration/Capabilities/make.ZLIB.defn > >> INC_DIRS += $(HDF5_INC_DIRS) > >> INC_DIRS_F += $(HDF5_INC_DIRS) > >> HDF5_BUILD = > >> HDF5_ENABLE_CXX = no > >> HDF5_ENABLE_FORTRAN = yes > >> LIBSZ_DIR = > >> LIBZ_DIR = > >> HDF5_INSTALL_DIR = > >> HDF5_DIR = /share/apps/hdf5-1.8.12 > >> HDF5_ENABLE_CXX = no > >> HDF5_ENABLE_FORTRAN = yes > >> HDF5_INC_DIRS > >> = /share/apps/hdf5-1.8.12/lib /share/apps/hdf5-1.8.12/include > >> /share/apps/openmpi-1.6.5/include > >> HDF5_LIB_DIRS > >> = /share/apps/hdf5-1.8.12/lib /share/apps/openmpi-1.6.5/lib > >> HDF5_LIBS = hdf5hl_fortran hdf5_fortran hdf5_hl hdf5 z > >> mpi mpi_cxx open-rte open-pal dl nsl util m z > >> HAVE_CAPABILITY_HDF5 = 1 > >>> > >>> configs/sim/bindings/Configuration/Capabilities/make.HDF5.deps > >> > >> include > >> /home/dgarriso/Cactus/configs/fixedmhd/bindings/Configuration/Capabilities/make.MPI.deps > >> include > >> /home/dgarriso/Cactus/configs/fixedmhd/bindings/Configuration/Capabilities/make.ZLIB.deps > >> > >>> > >>> as well as > >>> > >>> confis/sim/config-info (as well as the option list that you > >>> used)? > >> > >> # CONFIGURATION : fixedmhd > >> # CONFIG-DATE : Mon Mar 19 01:07:33 2018 (GMT) > >> # CONFIG-HOST : cusco.hpcc.uh.edu > >> # CONFIG-STATUS : 0 > >> # CONFIG-OPTIONS : > >> CC=icc > >> CPPFLAGS=-DCCTK_DISABLE_OMP_COLLAPSE > >> CXX=icpc > >> CXX_OPTIMISE_FLAGS=-Os -ip -pthread -no-prec-div > >> C_OPTIMISE_FLAGS=-Os -ip -pthread -no-prec-div > >> F77=ifort > >> F77_OPTIMISE_FLAGS=-Os -ip -no-prec-div > >> F90=ifort > >> F90_OPTIMISE_FLAGS=-Os -ip -no-prec-div > >> FFLAGS=-O3 -fast -Mipa=fast,inline -tp=x64 > >> FFTW=yes > >> FFTW_DIR=/home/dgarriso/fftw3 > >> FFTW_LIBS=fftw3_threads fftw3_mpi $(MPI_LIBS) fftw3 m > >> FPPFLAGS=-DCCTK_DISABLE_OMP_COLLAPSE > >> HDF5_DIR=/share/apps/hdf5-1.8.12 > >> LAPACK=yes > >> LAPACK_DIR=/home/dgarriso/ifort64/lib > >> LAPACK_LIBS=acml ifcoremt_pic imf irc svml > >> MPI_DIR=/share/apps/openmpi-1.6.5 > >> MPI_INC_DIRS=/share/apps/openmpi-1.6.5/include > >> MPI_LIBS=mpi mpi_cxx open-rte open-pal dl nsl util > >> MPI_LIB_DIRS=/share/apps/openmpi-1.6.5/lib > >> OPTIMISE=yes > >> PTHREADS=no > >> VERBOSE=yes > >> > >>> > >>> If possible also the full output of: > >>> > >>> export VERBOSE=yes > >>> simfactory/bin/sim build 2>&1 | tee make.log > >>> > >>> or > >>> > >>> export VERBOSE=yes > >>> make sim 2>&1 | tee make.log > >>> > >>> (depending on whether you used simfactory or not), please? > >>> > >>> Yours, > >>> Roland > >>> > >>>> Hello, > >>>> > >>>> Every time I try to compile my code I get the following error. > >>>> > >>>> COMPILING arrangements/CactusPUGHIO/IOHDF5Util/src/Startup.c > >>>> /share/apps/hdf5-1.8.12/include/H5public.h(61): catastrophic > >>>> error: cannot open source file "mpi.h" # include <mpi.h> > >>>> > >>>> This is new as of the most recent versions of Cactus. Previous > >>>> compilations of the same code on the same cluster did not result > >>>> in this error. Any help is appreciated. > >>>> > >>>> I used the config option: MPI_DIR = BUILD > >>>> > >>>> -DG > >>>> > >>>> Sent from my iPhone > >>>> _______________________________________________ > >>>> Users mailing list > >>>> [email protected] > >>>> http://lists.einsteintoolkit.org/mailman/listinfo/users > >>> > >>> > >>> Yours, > >>> Roland > >>> > >>> > >>> -- > >>> My email is as private as my paper mail. I therefore support > >>> encrypting and signing email messages. Get my PGP key from > >>> http://pgp.mit.edu . > >> > > > > > > > > -- > > My email is as private as my paper mail. I therefore support > > encrypting and signing email messages. Get my PGP key from > > http://pgp.mit.edu . > > -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://pgp.mit.edu .
pgpAqSJbFDVpe.pgp
Description: OpenPGP digital signature
_______________________________________________ Users mailing list [email protected] http://lists.einsteintoolkit.org/mailman/listinfo/users
