[OMPI users] fatal error for openmpi-master-201704200300-ded63c with SuSE Linux and gcc-6.3.0

[Siegmar Gross]

Hi,

I tried to install openmpi-master-201704200300-ded63c on my "SUSE Linux
Enterprise Server 12.2 (x86_64)" with Sun C 5.14 and gcc-6.3.0.
Unfortunately, "make" breaks with the following error for gcc. I've had
no problems with cc.


loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 136 grep topology
log.make.Linux.x86_64.64_gcc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
CC topology-custom.lo
CC topology-xml.lo
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-nvml.c:14:18:
fatal error: nvml.h: No such file or directory
Makefile:2181: recipe for target 'topology-nvml.lo' failed
make[4]: *** [topology-nvml.lo] Error 1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137





loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137 grep topology
../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/log.make.Linux.x86_64.64_cc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-synthetic.c",
line 851: warning: initializer will be sign-extended: -1
CC topology-custom.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-custom.c",
line 88: warning: initializer will be sign-extended: -1
CC topology-xml.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-xml.c",
line 1815: warning: initializer will be sign-extended: -1
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
CC topology-linux.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c",
line 2919: warning: initializer will be sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c",
line 2919: warning: initializer will be sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c",
line 2919: warning: initializer will be sign-extended: -1
CC topology-hardwired.lo
CC topology-x86.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-x86.c",
line 122: warning: initializer will be sign-extended: -1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 138




I used the following commands to configure the package.

loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 145 head -7
config.log |tail -1
$ ../openmpi-master-201704200300-ded63c5/configure
--prefix=/usr/local/openmpi-master_64_gcc
--libdir=/usr/local/openmpi-master_64_gcc/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 CC=gcc CXX=g++ FC=gfortran
CFLAGS=-m64 CXXFLAGS=-m64 FCFLAGS=-m64 CPP=cpp CXXCPP=cpp --enable-mpi-cxx
--enable-cxx-exceptions --enable-mpi-java --with-cuda=/usr/local/cuda
--with-valgrind=/usr/local/valgrind --with-hwloc=internal --without-verbs
--with-wrapper-cflags=-std=c11 -m64 --with-wrapper-cxxflags=-m64
--with-wrapper-fcflags=-m64 --enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146




loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146 head -7
../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/config.log | tail -1
$ ../openmpi-master-201704200300-ded63c5/configure
--prefix=/usr/local/openmpi-master_64_cc
--libdir=/usr/local/openmpi-master_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
-L/usr/local/lib64 -L/usr/local/cuda/lib64 CC=cc CXX=CC FC=f95 CFLAGS=-m64 -mt
-I/usr/local/include -I/usr/local/cuda/include CXXFLAGS=-m64
-I/usr/local/include -I/usr/local/cuda/include FCFLAGS=-m64 CPP=cpp
-I/usr/local/include -I/usr/local/cuda/include CXXCPP=cpp -I/usr/local/include
-I/usr/local/cuda/include --enable-mpi-cxx --enable-cxx-exceptions
--enable-mpi-java --with-cuda=/usr/local/cuda
--with-valgrind=/usr/local/valgrind --with-hwloc=internal --without-verbs
--with-wrapper-cflags=-m64 -mt --with-wrapper-cxxflags=-m64
--with-wrapper-fcflags=-m64 --with-wrapper-ldflags=-mt --enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 147



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

[r***@open-mpi.org]

This is a known issue due to something in the NVIDIA library and it’s interactions with hwloc. Your tarball tag indicates you should have the attempted fix in it, so likely that wasn’t adequate. See https://github.com/open-mpi/ompi/pull/3283 <https://github.com/open-mpi/ompi/pull/3283> for the discussion

Post by Siegmar Gross
Hi,
I tried to install openmpi-master-201704200300-ded63c on my "SUSE Linux
Enterprise Server 12.2 (x86_64)" with Sun C 5.14 and gcc-6.3.0.
Unfortunately, "make" breaks with the following error for gcc. I've had
no problems with cc.
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 136 grep topology log.make.Linux.x86_64.64_gcc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
CC topology-custom.lo
CC topology-xml.lo
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-nvml.c:14:18: fatal error: nvml.h: No such file or directory
Makefile:2181: recipe for target 'topology-nvml.lo' failed
make[4]: *** [topology-nvml.lo] Error 1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137 grep topology ../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/log.make.Linux.x86_64.64_cc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-synthetic.c", line 851: warning: initializer will be sign-extended: -1
CC topology-custom.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-custom.c", line 88: warning: initializer will be sign-extended: -1
CC topology-xml.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-xml.c", line 1815: warning: initializer will be sign-extended: -1
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
CC topology-linux.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c", line 2919: warning: initializer will be sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c", line 2919: warning: initializer will be sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c", line 2919: warning: initializer will be sign-extended: -1
CC topology-hardwired.lo
CC topology-x86.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-x86.c", line 122: warning: initializer will be sign-extended: -1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 138
I used the following commands to configure the package.
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 145 head -7 config.log |tail -1
$ ../openmpi-master-201704200300-ded63c5/configure --prefix=/usr/local/openmpi-master_64_gcc --libdir=/usr/local/openmpi-master_64_gcc/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 CC=gcc CXX=g++ FC=gfortran CFLAGS=-m64 CXXFLAGS=-m64 FCFLAGS=-m64 CPP=cpp CXXCPP=cpp --enable-mpi-cxx --enable-cxx-exceptions --enable-mpi-java --with-cuda=/usr/local/cuda --with-valgrind=/usr/local/valgrind --with-hwloc=internal --without-verbs --with-wrapper-cflags=-std=c11 -m64 --with-wrapper-cxxflags=-m64 --with-wrapper-fcflags=-m64 --enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146 head -7 ../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/config.log | tail -1
$ ../openmpi-master-201704200300-ded63c5/configure --prefix=/usr/local/openmpi-master_64_cc --libdir=/usr/local/openmpi-master_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 -L/usr/local/lib64 -L/usr/local/cuda/lib64 CC=cc CXX=CC FC=f95 CFLAGS=-m64 -mt -I/usr/local/include -I/usr/local/cuda/include CXXFLAGS=-m64 -I/usr/local/include -I/usr/local/cuda/include FCFLAGS=-m64 CPP=cpp -I/usr/local/include -I/usr/local/cuda/include CXXCPP=cpp -I/usr/local/include -I/usr/local/cuda/include --enable-mpi-cxx --enable-cxx-exceptions --enable-mpi-java --with-cuda=/usr/local/cuda --with-valgrind=/usr/local/valgrind --with-hwloc=internal --without-verbs --with-wrapper-cflags=-m64 -mt --with-wrapper-cxxflags=-m64 --with-wrapper-fcflags=-m64 --with-wrapper-ldflags=-mt --enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 147
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
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Gilles Gouaillardet]

The PR simply disables nvml in hwloc is CUDA is disabled in Open MPI.

it also add cuda directory to CPPFLAGS, so there should be no need to
manually add -I/usr/local/cuda/include to CPPFLAGS.


Siegmar,

could you please post your config.log

also, is there a nvml.h file in /usr/local/cuda/include

last but not least, can you please run

make V=1

and post the output related to the compilation of topology-nvml.lo


Thanks and regards,


Gilles

This is a known issue due to something in the NVIDIA library and it’s
interactions with hwloc. Your tarball tag indicates you should have
the attempted fix in it, so likely that wasn’t adequate. See
https://github.com/open-mpi/ompi/pull/3283 for the discussion

On Apr 20, 2017, at 8:11 AM, Siegmar Gross
Hi,
I tried to install openmpi-master-201704200300-ded63c on my "SUSE Linux
Enterprise Server 12.2 (x86_64)" with Sun C 5.14 and gcc-6.3.0.
Unfortunately, "make" breaks with the following error for gcc. I've had
no problems with cc.
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 136 grep
topology log.make.Linux.x86_64.64_gcc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
CC topology-custom.lo
CC topology-xml.lo
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
fatal error: nvml.h: No such file or directory
Makefile:2181: recipe for target 'topology-nvml.lo' failed
make[4]: *** [topology-nvml.lo] Error 1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137 grep topology
../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/log.make.Linux.x86_64.64_cc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-synthetic.c",
line 851: warning: initializer will be sign-extended: -1
CC topology-custom.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-custom.c",
line 88: warning: initializer will be sign-extended: -1
CC topology-xml.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-xml.c",
line 1815: warning: initializer will be sign-extended: -1
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
CC topology-linux.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c",
line 2919: warning: initializer will be sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c",
line 2919: warning: initializer will be sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c",
line 2919: warning: initializer will be sign-extended: -1
CC topology-hardwired.lo
CC topology-x86.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-x86.c",
line 122: warning: initializer will be sign-extended: -1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 138
I used the following commands to configure the package.
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 145 head
-7 config.log |tail -1
$ ../openmpi-master-201704200300-ded63c5/configure
--prefix=/usr/local/openmpi-master_64_gcc
--libdir=/usr/local/openmpi-master_64_gcc/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 CC=gcc CXX=g++
FC=gfortran CFLAGS=-m64 CXXFLAGS=-m64 FCFLAGS=-m64 CPP=cpp CXXCPP=cpp
--enable-mpi-cxx --enable-cxx-exceptions --enable-mpi-java
--with-cuda=/usr/local/cuda --with-valgrind=/usr/local/valgrind
--with-hwloc=internal --without-verbs --with-wrapper-cflags=-std=c11
-m64 --with-wrapper-cxxflags=-m64 --with-wrapper-fcflags=-m64
--enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146 head -7
../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/config.log | tail -1
$ ../openmpi-master-201704200300-ded63c5/configure
--prefix=/usr/local/openmpi-master_64_cc
--libdir=/usr/local/openmpi-master_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 -L/usr/local/lib64 -L/usr/local/cuda/lib64 CC=cc
CXX=CC FC=f95 CFLAGS=-m64 -mt -I/usr/local/include
-I/usr/local/cuda/include CXXFLAGS=-m64 -I/usr/local/include
-I/usr/local/cuda/include FCFLAGS=-m64 CPP=cpp -I/usr/local/include
-I/usr/local/cuda/include CXXCPP=cpp -I/usr/local/include
-I/usr/local/cuda/include --enable-mpi-cxx --enable-cxx-exceptions
--enable-mpi-java --with-cuda=/usr/local/cuda
--with-valgrind=/usr/local/valgrind --with-hwloc=internal
--without-verbs --with-wrapper-cflags=-m64 -mt
--with-wrapper-cxxflags=-m64 --with-wrapper-fcflags=-m64
--with-wrapper-ldflags=-mt --enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 147
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
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Siegmar Gross]

Hi Gilles,

Post by Gilles Gouaillardet
The PR simply disables nvml in hwloc is CUDA is disabled in Open MPI.
it also add cuda directory to CPPFLAGS, so there should be no
need to manually add -I/usr/local/cuda/include to CPPFLAGS.
Siegmar,
could you please post your config.log
also, is there a nvml.h file in /usr/local/cuda/include

Yes, although cuda itself is a link to cuda-8.0.

loki root 86 ls -l /usr/local/cuda
lrwxrwxrwx 1 root root 8 Jan 31 13:57 /usr/local/cuda -> cuda-8.0
loki root 87 ls -l /usr/local/cuda/include/nvml.h
-rw-r--r-- 1 root root 221366 Sep 5 2016 /usr/local/cuda/include/nvml.h
loki root 88

Post by Gilles Gouaillardet
last but not least, can you please run
make V=1
and post the output related to the compilation of topology-nvml.lo

depbase=`echo topology-nvml.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../../../../../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I.
-I../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src -I../../../../../../opal/include -I../../../../../../ompi/include
-I../../../../../../oshmem/include -I../../../../../../opal/mca/hwloc/hwloc1116/hwloc/include/private/autogen
-I../../../../../../opal/mca/hwloc/hwloc1116/hwloc/include/hwloc/autogen -I../../../../../../ompi/mpiext/cuda/c
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116/hwloc/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/include -DHWLOC_INSIDE_LIBHWLOC
-DHWLOC_PLUGINS_PATH=\"/usr/local/openmpi-master_64_gcc/lib64/hwloc\" -DRUNSTATEDIR=\"\" -I../../../../../../../openmpi-master-201704200300-ded63c5
-I../../../../../.. -I../../../../../../../openmpi-master-201704200300-ded63c5/opal/include
-I../../../../../../../openmpi-master-201704200300-ded63c5/orte/include -I../../../../../../orte/include
-I../../../../../../../openmpi-master-201704200300-ded63c5/ompi/include -I../../../../../../../openmpi-master-201704200300-ded63c5/oshmem/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/event/libevent2022/libevent/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/event/libevent2022/libevent
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/event/libevent2022/libevent/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116/hwloc/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/include -I/usr/local/valgrind/include -fvisibility=hidden
-m64 -g -finline-functions -fno-strict-aliasing -fexceptions -mcx16 -pthread -MT topology-nvml.lo -MD -MP -MF $depbase.Tpo -c -o topology-nvml.lo
../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-nvml.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src
-I../../../../../../opal/include -I../../../../../../ompi/include -I../../../../../../oshmem/include
-I../../../../../../opal/mca/hwloc/hwloc1116/hwloc/include/private/autogen -I../../../../../../opal/mca/hwloc/hwloc1116/hwloc/include/hwloc/autogen
-I../../../../../../ompi/mpiext/cuda/c
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116/hwloc/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/include -DHWLOC_INSIDE_LIBHWLOC
-DHWLOC_PLUGINS_PATH=\"/usr/local/openmpi-master_64_gcc/lib64/hwloc\" -DRUNSTATEDIR=\"\" -I../../../../../../../openmpi-master-201704200300-ded63c5
-I../../../../../.. -I../../../../../../../openmpi-master-201704200300-ded63c5/opal/include
-I../../../../../../../openmpi-master-201704200300-ded63c5/orte/include -I../../../../../../orte/include
-I../../../../../../../openmpi-master-201704200300-ded63c5/ompi/include -I../../../../../../../openmpi-master-201704200300-ded63c5/oshmem/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/event/libevent2022/libevent/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/event/libevent2022/libevent
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/event/libevent2022/libevent/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116/hwloc/include
-I/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/include -I/usr/local/valgrind/include -fvisibility=hidden -m64
-g -finline-functions -fno-strict-aliasing -fexceptions -mcx16 -pthread -MT topology-nvml.lo -MD -MP -MF .deps/topology-nvml.Tpo -c
../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-nvml.c -fPIC -DPIC -o .libs/topology-nvml.o
../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-nvml.c:14:18: fatal error: nvml.h: No such file or directory
#include <nvml.h>
^
compilation terminated.
Makefile:2181: recipe for target 'topology-nvml.lo' failed
make[4]: *** [topology-nvml.lo] Error 1
make[4]: Leaving directory '/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116/hwloc/src'
Makefile:1846: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116/hwloc'
Makefile:2010: recipe for target 'all-recursive' failed
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory '/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal/mca/hwloc/hwloc1116'
Makefile:2380: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/export2/src/openmpi-master/openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc/opal'
Makefile:1897: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1


Kind regards and thank you very much for your help

Siegmar

Post by Gilles Gouaillardet
Thanks and regards,
Gilles

Post by r***@open-mpi.org
This is a known issue due to something in the NVIDIA library and it’s interactions with hwloc. Your tarball tag indicates you should have the attempted fix in
it, so likely that wasn’t adequate. See https://github.com/open-mpi/ompi/pull/3283 for the discussion

Post by Siegmar Gross
Hi,
I tried to install openmpi-master-201704200300-ded63c on my "SUSE Linux
Enterprise Server 12.2 (x86_64)" with Sun C 5.14 and gcc-6.3.0.
Unfortunately, "make" breaks with the following error for gcc. I've had
no problems with cc.
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 136 grep topology log.make.Linux.x86_64.64_gcc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
CC topology-custom.lo
CC topology-xml.lo
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-nvml.c:14:18: fatal error: nvml.h: No such file or
directory
Makefile:2181: recipe for target 'topology-nvml.lo' failed
make[4]: *** [topology-nvml.lo] Error 1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 137 grep topology
../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/log.make.Linux.x86_64.64_cc
CC topology.lo
CC topology-noos.lo
CC topology-synthetic.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-synthetic.c", line 851: warning: initializer will be
sign-extended: -1
CC topology-custom.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-custom.c", line 88: warning: initializer will be
sign-extended: -1
CC topology-xml.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-xml.c", line 1815: warning: initializer will be
sign-extended: -1
CC topology-xml-nolibxml.lo
CC topology-pci.lo
CC topology-nvml.lo
CC topology-linux.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c", line 2919: warning: initializer will be
sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c", line 2919: warning: initializer will be
sign-extended: -1
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-linux.c", line 2919: warning: initializer will be
sign-extended: -1
CC topology-hardwired.lo
CC topology-x86.lo
"../../../../../../../openmpi-master-201704200300-ded63c5/opal/mca/hwloc/hwloc1116/hwloc/src/topology-x86.c", line 122: warning: initializer will be
sign-extended: -1
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 138
I used the following commands to configure the package.
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 145 head -7 config.log |tail -1
$ ../openmpi-master-201704200300-ded63c5/configure --prefix=/usr/local/openmpi-master_64_gcc --libdir=/usr/local/openmpi-master_64_gcc/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 CC=gcc CXX=g++
FC=gfortran CFLAGS=-m64 CXXFLAGS=-m64 FCFLAGS=-m64 CPP=cpp CXXCPP=cpp --enable-mpi-cxx --enable-cxx-exceptions --enable-mpi-java --with-cuda=/usr/local/cuda
--with-valgrind=/usr/local/valgrind --with-hwloc=internal --without-verbs --with-wrapper-cflags=-std=c11 -m64 --with-wrapper-cxxflags=-m64
--with-wrapper-fcflags=-m64 --enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 146 head -7 ../openmpi-master-201704200300-ded63c5-Linux.x86_64.64_cc/config.log | tail -1
$ ../openmpi-master-201704200300-ded63c5/configure --prefix=/usr/local/openmpi-master_64_cc --libdir=/usr/local/openmpi-master_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 -L/usr/local/lib64 -L/usr/local/cuda/lib64 CC=cc CXX=CC FC=f95 CFLAGS=-m64 -mt -I/usr/local/include -I/usr/local/cuda/include CXXFLAGS=-m64
-I/usr/local/include -I/usr/local/cuda/include FCFLAGS=-m64 CPP=cpp -I/usr/local/include -I/usr/local/cuda/include CXXCPP=cpp -I/usr/local/include
-I/usr/local/cuda/include --enable-mpi-cxx --enable-cxx-exceptions --enable-mpi-java --with-cuda=/usr/local/cuda --with-valgrind=/usr/local/valgrind
--with-hwloc=internal --without-verbs --with-wrapper-cflags=-m64 -mt --with-wrapper-cxxflags=-m64 --with-wrapper-fcflags=-m64 --with-wrapper-ldflags=-mt
--enable-debug
loki openmpi-master-201704200300-ded63c5-Linux.x86_64.64_gcc 147
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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