[OMPI users] problem with opal_list_remove_item for openmpi-v2.x-201702010255-8b16747 on Linux

Jeff Squyres (jsquyres)

2017-02-03 14:00:06 UTC

I've filed this as https://github.com/open-mpi/ompi/issues/2920.

Ralph is just heading out for about a week or so; it may not get fixed until he comes back.

Post by Siegmar Gross
Hi,
I have installed openmpi-v2.x-201702010255-8b16747 on my "SUSE Linux
Enterprise Server 12.2 (x86_64)" with Sun C 5.14 and gcc-6.3.0.
Unfortunately, I get a warning from "opal_list_remove_item" about a
missing item when I run one of my programs.
loki spawn 115 mpiexec -np 1 --host loki,loki,nfs1 spawn_intra_comm
Parent process 0: I create 2 slave processes
Parent process 0 running on loki
MPI_COMM_WORLD ntasks: 1
COMM_CHILD_PROCESSES ntasks_local: 1
COMM_CHILD_PROCESSES ntasks_remote: 2
COMM_ALL_PROCESSES ntasks: 3
mytid in COMM_ALL_PROCESSES: 0
Child process 0 running on loki
MPI_COMM_WORLD ntasks: 2
COMM_ALL_PROCESSES ntasks: 3
mytid in COMM_ALL_PROCESSES: 1
Child process 1 running on nfs1
MPI_COMM_WORLD ntasks: 2
COMM_ALL_PROCESSES ntasks: 3
mytid in COMM_ALL_PROCESSES: 2
Warning :: opal_list_remove_item - the item 0xc45f80 is not on the list 0x7f5bb1f34978
loki spawn 116
I used the following commands to build and install the package.
${SYSTEM_ENV} is "Linux" and ${MACHINE_ENV} is "x86_64" for my
Linux machine. Option "--enable-mpi-cxx-bindings is now
unrecognized. Are cxx-bindings now automatically supported?
"configure" reports a warning that I should report.
mkdir openmpi-v2.x-201702010255-8b16747-${SYSTEM_ENV}.${MACHINE_ENV}.64_cc
cd openmpi-v2.x-201702010255-8b16747-${SYSTEM_ENV}.${MACHINE_ENV}.64_cc
../openmpi-v2.x-201702010255-8b16747/configure \
--prefix=/usr/local/openmpi-2.1.0_64_cc \
--libdir=/usr/local/openmpi-2.1.0_64_cc/lib64 \
--with-jdk-bindir=/usr/local/jdk1.8.0_66/bin \
--with-jdk-headers=/usr/local/jdk1.8.0_66/include \
JAVA_HOME=/usr/local/jdk1.8.0_66 \
LDFLAGS="-m64 -mt -Wl,-z -Wl,noexecstack" CC="cc" CXX="CC" FC="f95" \
CFLAGS="-m64 -mt" CXXFLAGS="-m64" FCFLAGS="-m64" \
CPP="cpp" CXXCPP="cpp" \
--enable-mpi-cxx \
--enable-mpi-cxx-bindings \
--enable-cxx-exceptions \
--enable-mpi-java \
--enable-mpi-thread-multiple \
--with-hwloc=internal \
--without-verbs \
--with-wrapper-cflags="-m64 -mt" \
--with-wrapper-cxxflags="-m64" \
--with-wrapper-fcflags="-m64" \
--with-wrapper-ldflags="-mt" \
--enable-debug \
|& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_cc
make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_cc
rm -r /usr/local/openmpi-2.1.0_64_cc.old
mv /usr/local/openmpi-2.1.0_64_cc /usr/local/openmpi-2.1.0_64_cc.old
make install |& tee log.make-install.$SYSTEM_ENV.$MACHINE_ENV.64_cc
make check |& tee log.make-check.$SYSTEM_ENV.$MACHINE_ENV.64_cc
...
checking numaif.h usability... no
checking numaif.h presence... yes
configure: WARNING: numaif.h: present but cannot be compiled
configure: WARNING: numaif.h: check for missing prerequisite headers?
configure: WARNING: numaif.h: see the Autoconf documentation
configure: WARNING: numaif.h: section "Present But Cannot Be Compiled"
configure: WARNING: numaif.h: proceeding with the compiler's result
configure: WARNING: ## ------------------------------------------------------ ##
configure: WARNING: ## Report this to http://www.open-mpi.org/community/help/ ##
configure: WARNING: ## ------------------------------------------------------ ##
checking for numaif.h... no
...
I would be grateful, if somebody can fix the problems. do you need anything
else? Thank you very much for any help in advance.
Kind regards
Siegmar
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--
Jeff Squyres
***@cisco.com