[OMPI users] error building openmpi-master-201810310352-a1e85b0 on Linux with Sun C

[Siegmar Gross]

Hi,

I've tried to install openmpi-master-201810310352-a1e85b0 on my "SUSE Linux
Enterprise Server 12.3 (x86_64)" with Sun C 5.15 (Oracle Developer Studio
12.6). Unfortunately, I still get the following error that I reported some
time ago.

https://users.open-mpi.narkive.com/lvQKElru/ompi-users-error-building-openmpi-master-201810050304-5f1c940-on-linux-with-sun-c


loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125 head -7
config.log | tail -1
$ ../openmpi-master-201810310352-a1e85b0/configure
--prefix=/usr/local/openmpi-master_64_cc
--libdir=/usr/local/openmpi-master_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 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-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125


loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125 tail -27
log.make.Linux.x86_64.64_cc
Making all in tools/wrappers
make[2]: Entering directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers'
GENERATE opal_wrapper.1
CC opal_wrapper.o
CCLD opal_wrapper
/usr/bin/ld: opal_wrapper.o: in function `opal_atomic_mb':
/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers//../../../../openmpi-master-201810310352-a1e85b0/opal/include/opal/sys/atomic_stdc.h:64:
undefined reference to `atomic_thread_fence'
/usr/bin/ld: opal_wrapper.o: in function `opal_atomic_wmb':
/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers//../../../../openmpi-master-201810310352-a1e85b0/opal/include/opal/sys/atomic_stdc.h:69:
undefined reference to `atomic_thread_fence'
/usr/bin/ld: opal_wrapper.o: in function `opal_atomic_rmb':
/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers//../../../../openmpi-master-201810310352-a1e85b0/opal/include/opal/sys/atomic_stdc.h:74:
undefined reference to `atomic_thread_fence'
/usr/bin/ld: opal_wrapper.o: in function `opal_atomic_lock_init':
/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers//../../../../openmpi-master-201810310352-a1e85b0/opal/include/opal/sys/atomic_stdc.h:210:
undefined reference to `atomic_flag_clear'
/usr/bin/ld: opal_wrapper.o: in function `opal_atomic_trylock':
/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers//../../../../openmpi-master-201810310352-a1e85b0/opal/include/opal/sys/atomic_stdc.h:216:
undefined reference to `atomic_flag_test_and_set'
/usr/bin/ld: opal_wrapper.o: in function `opal_atomic_unlock':
/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers//../../../../openmpi-master-201810310352-a1e85b0/opal/include/opal/sys/atomic_stdc.h:229:
undefined reference to `atomic_flag_clear'
postopt: error: ld failed to link the binary
cc: postopt failed for .libs/opal_wrapper
Makefile:1873: recipe for target 'opal_wrapper' failed
make[2]: *** [opal_wrapper] Error 2
make[2]: Leaving directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers'
Makefile:2377: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal'
Makefile:1895: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 126


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

[Kawashima, Takahiro]

Hi Siegmar,

According to the man page of cc in Oracle Developer Studio 12.6,
any atomics support runtime library is not linked by default.
Probably you'll need -xatomic=studio, -xatomic=gcc, or -latomic option.
I'm not sure whether the option should be added by Open MPI configure or by users.

https://docs.oracle.com/cd/E77782_01/html/E77803/cc-1.html
(see description of the -xatomic option)

Regards,
Takahiro Kawashima,
Fujitsu

Post by Siegmar Gross
Hi,
I've tried to install openmpi-master-201810310352-a1e85b0 on my "SUSE Linux
Enterprise Server 12.3 (x86_64)" with Sun C 5.15 (Oracle Developer Studio
12.6). Unfortunately, I still get the following error that I reported some
time ago.
https://users.open-mpi.narkive.com/lvQKElru/ompi-users-error-building-openmpi-master-201810050304-5f1c940-on-linux-with-sun-c
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125 head -7
config.log | tail -1
$ ../openmpi-master-201810310352-a1e85b0/configure
--prefix=/usr/local/openmpi-master_64_cc
--libdir=/usr/local/openmpi-master_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 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-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125 tail -27
log.make.Linux.x86_64.64_cc
Making all in tools/wrappers
make[2]: Entering directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers'
GENERATE opal_wrapper.1
CC opal_wrapper.o
CCLD opal_wrapper
undefined reference to `atomic_thread_fence'
undefined reference to `atomic_thread_fence'
undefined reference to `atomic_thread_fence'
undefined reference to `atomic_flag_clear'
undefined reference to `atomic_flag_test_and_set'
undefined reference to `atomic_flag_clear'
postopt: error: ld failed to link the binary
cc: postopt failed for .libs/opal_wrapper
Makefile:1873: recipe for target 'opal_wrapper' failed
make[2]: *** [opal_wrapper] Error 2
make[2]: Leaving directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers'
Makefile:2377: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal'
Makefile:1895: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 126
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

[Siegmar Gross]

Hi Takahiro,

thank you very much for your help. Adding "-xatomic=studio" to
CFLAGS solved the problem. Now I get a new error which I will
report in a separate email.

Kind regards

Siegmar

Post by Kawashima, Takahiro
Hi Siegmar,
According to the man page of cc in Oracle Developer Studio 12.6,
any atomics support runtime library is not linked by default.
Probably you'll need -xatomic=studio, -xatomic=gcc, or -latomic option.
I'm not sure whether the option should be added by Open MPI configure or by users.
https://docs.oracle.com/cd/E77782_01/html/E77803/cc-1.html
(see description of the -xatomic option)
Regards,
Takahiro Kawashima,
Fujitsu

Post by Siegmar Gross
Hi,
I've tried to install openmpi-master-201810310352-a1e85b0 on my "SUSE Linux
Enterprise Server 12.3 (x86_64)" with Sun C 5.15 (Oracle Developer Studio
12.6). Unfortunately, I still get the following error that I reported some
time ago.
https://users.open-mpi.narkive.com/lvQKElru/ompi-users-error-building-openmpi-master-201810050304-5f1c940-on-linux-with-sun-c
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125 head -7
config.log | tail -1
$ ../openmpi-master-201810310352-a1e85b0/configure
--prefix=/usr/local/openmpi-master_64_cc
--libdir=/usr/local/openmpi-master_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 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-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 125 tail -27
log.make.Linux.x86_64.64_cc
Making all in tools/wrappers
make[2]: Entering directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers'
GENERATE opal_wrapper.1
CC opal_wrapper.o
CCLD opal_wrapper
undefined reference to `atomic_thread_fence'
undefined reference to `atomic_thread_fence'
undefined reference to `atomic_thread_fence'
undefined reference to `atomic_flag_clear'
undefined reference to `atomic_flag_test_and_set'
undefined reference to `atomic_flag_clear'
postopt: error: ld failed to link the binary
cc: postopt failed for .libs/opal_wrapper
Makefile:1873: recipe for target 'opal_wrapper' failed
make[2]: *** [opal_wrapper] Error 2
make[2]: Leaving directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal/tools/wrappers'
Makefile:2377: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
'/export2/src/openmpi-master/openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc/opal'
Makefile:1895: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1
loki openmpi-master-201810310352-a1e85b0-Linux.x86_64.64_cc 126
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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