Hello DG,
it looks like you are trying to use the system mpicc to compile OpenMPI in Cactus' ExternalLibraries.
This is a very odd thing to do and I am not surprised that you would fail attempting this.
Instead why not set MPI_DIR = <PATH-TO-DIRECTORY-WHERE-MPICC-IC>/.. ie the parent directory of the system MPI's "bin" directory? Leave the other MPI settings blank and Cactus should obtain the required settings from the system MPI that it will find in MPI_DIR.
Yours, Roland
Hello,
Using mpicc, etc… seems to work a lot better but I’m still having a couple issues. When I use the cluster’s mpi, I get the error
ld: cannot find -lmpi_usempif08 make[2]: *** [/home/dgarriso/Cactus/exe/cactus_fixedmhd] Error 1 make[1]: *** [fixedmhd] Error 2 make: *** [fixedmhd-rebuild] Error 2
When I try to build the Cactus mpi, it fails
Making all in libevent Making all in . libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT event.lo -MD -MP -MF .deps/event.Tpo -c event.c -o event.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT evthread.lo -MD -MP -MF .deps/evthread.Tpo -c evthread.c -o evthread.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT evmap.lo -MD -MP -MF .deps/evmap.Tpo -c evmap.c -o evmap.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT log.lo -MD -MP -MF .deps/log.Tpo -c log.c -o log.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT evutil.lo -MD -MP -MF .deps/evutil.Tpo -c evutil.c -o evutil.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT evutil_rand.lo -MD -MP -MF .deps/evutil_rand.Tpo -c evutil_rand.c -o evutil_rand.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT strlcpy.lo -MD -MP -MF .deps/strlcpy.Tpo -c strlcpy.c -o strlcpy.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT select.lo -MD -MP -MF .deps/select.Tpo -c select.c -o select.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT poll.lo -MD -MP -MF .deps/poll.Tpo -c poll.c -o poll.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT epoll.lo -MD -MP -MF .deps/epoll.Tpo -c epoll.c -o epoll.o libtool: compile: mpiicc -DHAVE_CONFIG_H -I. -I./compat -I./include -I./include -DCCTK_DISABLE_OMP_COLLAPSE -D_XOPEN_SOURCE -D_XOPEN_SOURCE_EXTENDED -std=c99 -Os -ip -pthread -no-prec-div -Wall -fno-strict-aliasing -MT signal.lo -MD -MP -MF .deps/signal.Tpo -c signal.c -o signal.o signal.c(135): error: identifier "NSIG" is undefined int ncaught[NSIG]; ^
signal.c(253): error: identifier "SA_RESTART" is undefined sa.sa_flags |= SA_RESTART; ^
signal.c(281): error: identifier "NSIG" is undefined EVUTIL_ASSERT(evsignal >= 0 && evsignal < NSIG); ^
signal.c(355): error: identifier "NSIG" is undefined EVUTIL_ASSERT(evsignal >= 0 && evsignal < NSIG); ^
signal.c(409): error: identifier "NSIG" is undefined for (i = 0; i < NSIG; ++i) { ^
compilation aborted for signal.c (code 2) make[10]: *** [signal.lo] Error 1 make[9]: *** [all-recursive] Error 1 make[8]: *** [all] Error 2 make[7]: *** [all-recursive] Error 1 make[6]: *** [all-recursive] Error 1 make[5]: *** [all-recursive] Error 1 Died at /home/dgarriso/Cactus/arrangements/ExternalLibraries/MPI/src/build.pl line 74. make[4]: *** [/home/dgarriso/Cactus/configs/fixedmhd/scratch/done/MPI] Error 17 make[3]: *** [make.checked] Error 2 make[2]: *** [/home/dgarriso/Cactus/configs/fixedmhd/lib/libthorn_MPI.a] Error 2 make[1]: *** [fixedmhd] Error 2 make: *** [fixedmhd-rebuild] Error 2
Is this an issue with the cluster mpi installation or with how cactus works with the compilers? I am using Intel compilers from 2015 (intel/ics-2015-64-bit), and openmpi version 1.6.5 on the cluster compiled with intel compilers.
-DG
On Mar 21, 2018, at 9:52 AM, Roland Haas rhaas@illinois.edu 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 roland.haas@physics.gatech.edu 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
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Yours, Roland
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