Hi,
I've installed openmpi-v4.0.x-201903220241-97aa434 on my "SUSE Linux Enterprise
Server 12.3 (x86_64)" with Sun C 5.15 (Oracle Developer Studio 12.6).
Unfortunately, I get the following error for one of my small programs, although
I've configured with "-xatomic=studio" and "make" didn't show any errors. In the
past I didn't need the option and the program worked.
loki hello_1 130 ompi_info | grep "Configure command line:"
Configure command line: '--prefix=/usr/local/openmpi-4.0.1_64_cc'
'--libdir=/usr/local/openmpi-4.0.1_64_cc/lib64'
'--with-jdk-bindir=/usr/local/jdk-11/bin'
'--with-jdk-headers=/usr/local/jdk-11/include' 'JAVA_HOME=/usr/local/jdk-11'
'LDFLAGS=-m64 -mt -Wl,-z -Wl,noexecstack -L/usr/local/lib64' 'CC=cc' 'CXX=CC'
'FC=f95' 'CFLAGS=-m64 -mt -xatomic=studio' 'CXXFLAGS=-m64' 'FCFLAGS=-m64'
'CPP=cpp' 'CXXCPP=cpp' '--disable-mpi-fortran' '--enable-mpi-cxx'
'--enable-cxx-exceptions' '--enable-mpi-java'
'--with-valgrind=/usr/local/valgrind' '--with-hwloc=internal' '--without-verbs'
'--with-wrapper-cflags=-std=c11 -m64 -mt' '--with-wrapper-cxxflags=-m64'
'--with-wrapper-fcflags=-m64' '--with-wrapper-ldflags=-mt' '--enable-debug'
loki openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc 132 tail
log.make.Linux.x86_64.64_cc
CC spc_test.o
CCLD spc_test
make[2]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/test/spc'
make[2]: Entering directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/test'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/test'
make[1]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/test'
make[1]: Entering directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc'
loki openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc 133
loki hello_1 131 mpiexec -np 2 --host loki:2 hello_1_mpi
hello_1_mpi: symbol lookup error:
/usr/local/openmpi-4.0.1_64_cc/lib64/openmpi/mca_pmix_pmix3x.so: undefined
symbol: atomic_thread_fence
hello_1_mpi: symbol lookup error:
/usr/local/openmpi-4.0.1_64_cc/lib64/openmpi/mca_pmix_pmix3x.so: undefined
symbol: atomic_thread_fence
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus
causing
the job to be terminated. The first process to do so was:
Process name: [[61126,1],0]
Exit code: 127
--------------------------------------------------------------------------
loki hello_1 132
The man page states that I should also add option "-std=c11", but in that case
the build process breaks with the following error.
loki openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc 124 tail -35
log.make.Linux.x86_64.64_cc
libtool: compile: cc -DHAVE_CONFIG_H -I.
-I../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent
-I../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/compat
-I../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/include
-I./include -I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434/opal/include
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal/mca/hwloc/hwloc201/hwloc/include
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434/opal/mca/hwloc/hwloc201/hwloc/include
-Drandom=opal_random -std=c11 -m64 -mt -xatomic=studio -c
../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/evthread_pthread.c
-KPIC -DPIC -o .libs/evthread_pthread.o
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 135: undefined symbol: NSIG
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 214: incomplete struct/union/enum sigaction: sa
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 243: incomplete struct/union/enum sigaction: sizeof()
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 251: incomplete struct/union/enum sigaction: sizeof()
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 252: undefined struct/union member: sa_handler
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 252: warning: improper pointer/integer combination: op "="
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 253: undefined struct/union member: sa_flags
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 253: undefined symbol: SA_RESTART
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 254: warning: implicit function declaration: sigfillset
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 254: undefined struct/union member: sa_mask
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 256: warning: implicit function declaration: sigaction
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 281: undefined symbol: NSIG
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 355: undefined symbol: NSIG
"../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c",
line 409: undefined symbol: NSIG
cc: acomp failed for
../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/signal.c
Makefile:772: recipe for target 'signal.lo' failed
make[5]: *** [signal.lo] Error 1
make[5]: *** Waiting for unfinished jobs....
libtool: compile: cc -DHAVE_CONFIG_H -I.
-I../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent
-I../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/compat
-I../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/include
-I./include -I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434/opal/include
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal/mca/hwloc/hwloc201/hwloc/include
-I/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434/opal/mca/hwloc/hwloc201/hwloc/include
-Drandom=opal_random -std=c11 -m64 -mt -xatomic=studio -c
../../../../../../openmpi-v4.0.x-201903220241-97aa434/opal/mca/event/libevent2022/libevent/evthread_pthread.c
-o evthread_pthread.o >/dev/null 2>&1
make[5]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal/mca/event/libevent2022/libevent'
Makefile:792: recipe for target 'all-recursive' failed
make[4]: *** [all-recursive] Error 1
make[4]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal/mca/event/libevent2022/libevent'
Makefile:648: recipe for target 'all' failed
make[3]: *** [all] Error 2
make[3]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal/mca/event/libevent2022/libevent'
Makefile:2006: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal/mca/event/libevent2022'
Makefile:2375: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
'/export2/src/openmpi-4.0.1/openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc/opal'
Makefile:1893: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1
loki openmpi-v4.0.x-201903220241-97aa434-Linux.x86_64.64_cc 124
I would be grateful, if somebody can fix the problem. Do you need anything
else? Thank you very much for any help in advance.
Kind regards
Siegmar
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