October 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Problems in MPICH 3.1.3 installation in OSX 10.10 with ifort compiler and Xcode 6.1
by Junchao Zhang 28 Oct '14

28 Oct '14

I don't have Intel compilers for Mac OSX. But I succeeded in building mpich 3.1.3 with Yosemite + Xcode 6.1 + gcc/gfortran 4.9. --Junchao Zhang On Mon, Oct 27, 2014 at 6:49 PM, Alejandro de la Calle < alejandrodelacallenegro(a)gmail.com> wrote: > Hi there, > > I am trying to build mpich 3.1.3. in a Mac OSX 10.10 Yosemite with Xcode > 6.1 and intel compilers icc and ifort version 15.0.0 20140716. I get an > error when I am building the installation. The error is the following: > > GEN lib/libpmpi.la > ifort: command line warning #10006: ignoring unknown option > '-force_load,src/mpl/.libs/libmpl.a' > ifort: command line warning #10006: ignoring unknown option > '-force_load,/Users/alejandrodelacallenegro/Downloads/mpich-3.1.3/src/openpa/src/.libs/libopa.a' > ifort: command line warning #10006: ignoring unknown option > '-force_load,src/mpi/romio/.libs/libpromio.a' > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: > object: lib/.libs/libpmpi.a(initthread.o) malformed object (section > contents at offset 0 with a size of 1056, overlaps Mach-O headers at offset > 0 with a size of 768) > > I do not understand where the error come from, from the compiler or from > libtool. I have also attached the outputs of the configuration and the > build steps. > > Thanks for your time, > > Alex > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] ROMIO+Lustre problems in OpenMPI 1.8.3
by Rob Latham 28 Oct '14

28 Oct '14

On 10/28/2014 06:00 AM, Paul Kapinos wrote: > Dear Open MPI and ROMIO developer, > > We use Open MPI v.1.6.x and 1.8.x in our cluster. > We have Lustre file system; we wish to use MPI_IO. > So the OpenMPI's are compiled with this flag: > > --with-io-romio-flags='--with-file-system=testfs+ufs+nfs+lustre' > > In our newest installation openmpi/1.8.3 we found that MPI_IO is *broken*. > > Short seek for root of the evil bring the following to light: > > - the ROMIO component 'MCA io: romio' isn't here at all in the affected > version, because > > - configure of ROMIO has *failed* (cf. logs (a,b,c). > - because lustre_user.h was found but could not be compiled. lustre_user.h cannot be compiled because quota defines won't compile. Ugh, what a mess. A while back I noticed this and fixed it by removing an XOPEN_SOURCE feature test macro: http://trac.mpich.org/projects/mpich/ticket/1973 Then, on solaris with --enable-strict we needed to put *back* the XOPEN_SOURCE macro or else pread and pwrite would be undefined. So what I really need to to is delete XOPEN_SOURCE since it causes such headaches, and on the rare platforms that only have pread/pwrite defined if you take extraordinary measures, if at all, I'll have a ROMIO pread and pwrite that simply do seek + write (or read). For now, please delete the XOPEN_SOURCE line at the very beginning of src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c ==rob > > > In our system, there are two lustre_user.h available: > $ locate lustre_user.h > /usr/include/linux/lustre_user.h > /usr/include/lustre/lustre_user.h > As I'm not very convinient with lustre, I just attach both of them. > > pk224850@cluster:~[509]$ uname -a > Linux cluster.rz.RWTH-Aachen.DE 2.6.32-431.29.2.el6.x86_64 #1 SMP Tue > Sep 9 13:45:55 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux > > pk224850@cluster:~[510]$ cat /etc/issue > Scientific Linux release 6.5 (Carbon) > > Note that openmpi/1.8.1 seem to be fully OK (MPI_IO works) in our > environment. > > Best > > Paul Kapinos > > P.S. Is there a confugure flag, which will enforce ROMIO? That is when > ROMIO not available, configure would fail. This would make such hidden > errors publique at installation time.. > > > > > > > a) Log in Open MPI's config.log: > ------------------------------------------------------------------------------ > > configure:226781: OMPI configuring in ompi/mca/io/romio/romio > configure:226866: running /bin/sh './configure' > --with-file-system=testfs+ufs+nfs+lustre FROM_OMPI=yes CC="icc > -std=c99" CFLAGS="-DNDEBUG -O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 > -m64 -finline-functions -fno-strict-aliasing -restrict -fexceptions > -Qoption,cpp,--extended_float_types -pthread" CPPFLAGS=" > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/hwloc/hwloc172/hwloc/include > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent/include" > FFLAGS="-O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 -m64 " > LDFLAGS="-O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 -m64 > -fexceptions " --enable-shared --disable-static > --with-file-system=testfs+ufs+nfs+lustre > --prefix=/opt/MPI/openmpi-1.8.3/linux/intel --disable-aio > --cache-file=/dev/null --srcdir=. --disable-option-checking > configure:226876: /bin/sh './configure' *failed* for > ompi/mca/io/romio/romio > configure:226911: WARNING: ROMIO distribution did not configure > successfully > configure:227425: checking if MCA component io:romio can compile > configure:227427: result: no > ------------------------------------------------------------------------------ > > > > > b) dump of Open MPI's 'configure' output to the console: > ------------------------------------------------------------------------------ > > checking lustre/lustre_user.h usability... no > checking lustre/lustre_user.h presence... yes > configure: WARNING: lustre/lustre_user.h: present but cannot be compiled > configure: WARNING: lustre/lustre_user.h: check for missing > prerequisite headers? > configure: WARNING: lustre/lustre_user.h: see the Autoconf documentation > configure: WARNING: lustre/lustre_user.h: section "Present But > Cannot Be Compiled" > configure: WARNING: lustre/lustre_user.h: proceeding with the compiler's > result > configure: WARNING: ## -------------------------------- ## > configure: WARNING: ## Report this to discuss(a)mpich.org ## > configure: WARNING: ## -------------------------------- ## > checking for lustre/lustre_user.h... no > configure: error: LUSTRE support requested but cannot find > lustre/lustre_user.h header file > configure: /bin/sh './configure' *failed* for ompi/mca/io/romio/romio > configure: WARNING: ROMIO distribution did not configure successfully > checking if MCA component io:romio can compile... no > ------------------------------------------------------------------------------ > > > c) ompi/mca/io/romio/romio's config.log: > ------------------------------------------------------------------------------ > > configure:20962: checking lustre/lustre_user.h usability > configure:20962: icc -std=c99 -c -DNDEBUG -O3 -ip -axAVX,SSE4.2,SSE4.1 > -fp-model fast=2 -m64 -finline-functions -fno-strict-aliasing -restrict > -fexceptions -Qoption,cpp,--extended_float_types -pthread > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/hwloc/hwloc172/hwloc/include > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent/include > conftest.c >&5 > /usr/include/sys/quota.h(221): error: identifier "caddr_t" is undefined > caddr_t __addr) __THROW; > ^ > > compilation aborted for conftest.c (code 2) > configure:20962: $? = 2 > configure: failed program was: > | /* confdefs.h */ > | #define PACKAGE_NAME "ROMIO" > | #define PACKAGE_TARNAME "romio" > | #define PACKAGE_VERSION "Open MPI" > | #define PACKAGE_STRING "ROMIO Open MPI" > | #define PACKAGE_BUGREPORT "discuss(a)mpich.org" > | #define PACKAGE_URL "http://www.mpich.org/" > | #define PACKAGE "romio" > | #define VERSION "Open MPI" > | #define STDC_HEADERS 1 > | #define HAVE_SYS_TYPES_H 1 > | #define HAVE_SYS_STAT_H 1 > | #define HAVE_STDLIB_H 1 > | #define HAVE_STRING_H 1 > | #define HAVE_MEMORY_H 1 > | #define HAVE_STRINGS_H 1 > | #define HAVE_INTTYPES_H 1 > | #define HAVE_STDINT_H 1 > | #define HAVE_UNISTD_H 1 > | #define HAVE_DLFCN_H 1 > | #define LT_OBJDIR ".libs/" > | #define HAVE_MPI_OFFSET 1 > | #define HAVE_MEMALIGN 1 > | #define HAVE_UNISTD_H 1 > | #define HAVE_FCNTL_H 1 > | #define HAVE_MALLOC_H 1 > | #define HAVE_STDDEF_H 1 > | #define HAVE_SYS_TYPES_H 1 > | #define u_char unsigned char > | #define u_short unsigned short > | #define u_int unsigned int > | #define u_long unsigned long > | #define SIZEOF_INT 4 > | #define SIZEOF_VOID_P 8 > | #define INT_LT_POINTER 1 > | #define HAVE_INT_LT_POINTER 1 > | #define SIZEOF_LONG_LONG 8 > | #define HAVE_LONG_LONG_64 1 > | #define HAVE_MPI_LONG_LONG_INT 1 > | #define HAVE_MPI_INFO 1 > | #define ROMIO_NFS 1 > | #define ROMIO_UFS 1 > | #define ROMIO_TESTFS 1 > | /* end confdefs.h. */ > | #include <stdio.h> > | #ifdef HAVE_SYS_TYPES_H > | # include <sys/types.h> > | #endif > | #ifdef HAVE_SYS_STAT_H > | # include <sys/stat.h> > | #endif > | #ifdef STDC_HEADERS > | # include <stdlib.h> > | # include <stddef.h> > | #else > | # ifdef HAVE_STDLIB_H > | # include <stdlib.h> > | # endif > | #endif > | #ifdef HAVE_STRING_H > | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H > | # include <memory.h> > | # endif > | # include <string.h> > | #endif > | #ifdef HAVE_STRINGS_H > | # include <strings.h> > | #endif > | #ifdef HAVE_INTTYPES_H > | # include <inttypes.h> > | #endif > | #ifdef HAVE_STDINT_H > | # include <stdint.h> > | #endif > | #ifdef HAVE_UNISTD_H > | # include <unistd.h> > | #endif > | #include <lustre/lustre_user.h> > configure:20962: result: no > configure:20962: checking lustre/lustre_user.h presence > configure:20962: icc -std=c99 -E > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/hwloc/hwloc172/hwloc/include > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent > -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent/include > conftest.c > configure:20962: $? = 0 > configure:20962: result: yes > configure:20962: WARNING: lustre/lustre_user.h: present but cannot be > compiled > configure:20962: WARNING: lustre/lustre_user.h: check for missing > prerequisite headers? > configure:20962: WARNING: lustre/lustre_user.h: see the Autoconf > documentation > configure:20962: WARNING: lustre/lustre_user.h: section "Present But > Cannot Be Compiled" > configure:20962: WARNING: lustre/lustre_user.h: proceeding with the > compiler's result > configure:20962: checking for lustre/lustre_user.h > configure:20962: result: no > configure:20971: error: LUSTRE support requested but cannot find > lustre/lustre_user.h header file > ------------------------------------------------------------------------------ > > > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI process killed and SIGUSR1
by Lu, Huiwei 28 Oct '14

28 Oct '14

Sorry I was wrong. I can not connect the client to the server because of the configuration of my laptop. The code can run successfully on another machine. — Huiwei > On Oct 28, 2014, at 8:11 AM, Lu, Huiwei <huiweilu(a)mcs.anl.gov> wrote: > > Hi, Hirak, > > Your client is connecting using an empty portname. You should use the same portname published by the server to connect. > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] MPI process killed and SIGUSR1
by Lu, Huiwei 28 Oct '14

28 Oct '14

Hi, Hirak, Your client is connecting using an empty portname. You should use the same portname published by the server to connect. — Huiwei > On Oct 27, 2014, at 6:52 AM, Roy, Hirak <Hirak_Roy(a)mentor.com> wrote: > > Hi Wesley, > > Here is my server.c and client.c. > I have explicitly added ‘assert(0);’ in client.c. > However my receive hangs in server and does not complete. > > Could you please enlighten on this more. > > Thanks, > Hirak > > > #include <sys/types.h> > #include <unistd.h> > #include "mpi.h" > #include <stdio.h> > #include <assert.h> > #include <stdlib.h> > #include <fcntl.h> > > > int main (int argc, char* argv[]) > { > > MPI_Init (&argc, &argv); > MPI_Errhandler_set(MPI_COMM_WORLD,MPI_ERRORS_RETURN); > > char portname[MPI_MAX_PORT_NAME]; > MPI_Open_port(MPI_INFO_NULL, portname); > MPI_Publish_name("RandomSession", MPI_INFO_NULL, portname); > printf ("Successfully published portname : %s\n", portname); > MPI_Comm newComm ; > MPI_Comm_accept (portname, MPI_INFO_NULL, 0, MPI_COMM_SELF, &newComm); > printf ("Successfully connected to client\n"); > MPI_Errhandler_set(newComm, MPI_ERRORS_RETURN); > > printf ("Waiting on receive\n"); > int val = 0 ; > MPI_Status status; > int errcode = MPI_Recv(&val, 1, MPI_INT, 0, 99, newComm, &status); > int errclass ; > MPI_Error_class(errcode, &errclass); > if (errclass == MPI_SUCCESS) { > printf ("Received a message with tag 99\n"); > MPI_Comm_disconnect (&newComm); > printf ("Disconnected client\n"); > } else { > printf ("Receive error\n"); > } > > > MPI_Unpublish_name("RandomSession", MPI_INFO_NULL, portname); > MPI_Close_port(portname); > MPI_Finalize(); > > } > > > #include <sys/types.h> > #include <unistd.h> > #include "mpi.h" > #include <stdio.h> > #include <assert.h> > #include <stdlib.h> > #include <fcntl.h> > > > int main (int argc, char* argv[]) > { > MPI_Init (&argc, &argv); > MPI_Errhandler_set(MPI_COMM_WORLD,MPI_ERRORS_RETURN); > > char portname[MPI_MAX_PORT_NAME]; > if (MPI_Lookup_name("RandomSession", MPI_INFO_NULL, portname) == MPI_SUCCESS) { > printf ("Successfully got portname : %s\n", portname); > MPI_Comm newComm ; > MPI_Comm_connect (portname, MPI_INFO_NULL, 0, MPI_COMM_SELF, &newComm); > printf ("Successfully connected to server\n"); > MPI_Errhandler_set(newComm, MPI_ERRORS_RETURN); > > assert (0); > int val = 0 ; > MPI_Send(&val, 1, MPI_INT, 0, 99, newComm); > printf ("Send a message with tag 99\n"); > MPI_Comm_disconnect (&newComm); > printf ("Disconnected client\n"); > } > MPI_Finalize(); > } > MPICH Version: 3.0.4 > MPICH Release date: Wed Apr 24 10:08:10 CDT 2013 > MPICH Device: ch3:sock > MPICH configure: --prefix /home/jlevitt/local/mpich-3.0.4/linux_x86_64 --disable-f77 --disable-fc --disable-f90modules --disable-cxx --enable-fast=nochkmsg --enable-fast=notiming --enable-fast=ndebug --enable-fast=O3 --with-device=ch3:sock CFLAGS=-O3 -fPIC CXXFLAGS=-O3 -fPIC > MPICH CC: /u/prod/gnu/gcc/20121129/gcc-4.5.0-linux_x86_64/bin/gcc -O3 -fPIC -O3 > MPICH CXX: no -O3 -fPIC > MPICH F77: no > MPICH FC: no > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] Re : MPI process killed and SIGUSR1
by Wesley Bland 28 Oct '14

28 Oct '14

Ok. I don't see where you're killing a process. > On Oct 27, 2014, at 10:51 PM, Roy, Hirak <Hirak_Roy(a)mentor.com> wrote: > > Hi Wesley, > > This is related to the FT problem. > > Thanks, > Hirak > > > Is this still related to your FT problems or is this a separate problem? > > Thanks, > Wesley > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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ROMIO+Lustre problems in OpenMPI 1.8.3
by Paul Kapinos 28 Oct '14

28 Oct '14

Dear Open MPI and ROMIO developer, We use Open MPI v.1.6.x and 1.8.x in our cluster. We have Lustre file system; we wish to use MPI_IO. So the OpenMPI's are compiled with this flag: > --with-io-romio-flags='--with-file-system=testfs+ufs+nfs+lustre' In our newest installation openmpi/1.8.3 we found that MPI_IO is *broken*. Short seek for root of the evil bring the following to light: - the ROMIO component 'MCA io: romio' isn't here at all in the affected version, because - configure of ROMIO has *failed* (cf. logs (a,b,c). - because lustre_user.h was found but could not be compiled. In our system, there are two lustre_user.h available: $ locate lustre_user.h /usr/include/linux/lustre_user.h /usr/include/lustre/lustre_user.h As I'm not very convinient with lustre, I just attach both of them. pk224850@cluster:~[509]$ uname -a Linux cluster.rz.RWTH-Aachen.DE 2.6.32-431.29.2.el6.x86_64 #1 SMP Tue Sep 9 13:45:55 CDT 2014 x86_64 x86_64 x86_64 GNU/Linux pk224850@cluster:~[510]$ cat /etc/issue Scientific Linux release 6.5 (Carbon) Note that openmpi/1.8.1 seem to be fully OK (MPI_IO works) in our environment. Best Paul Kapinos P.S. Is there a confugure flag, which will enforce ROMIO? That is when ROMIO not available, configure would fail. This would make such hidden errors publique at installation time.. a) Log in Open MPI's config.log: ------------------------------------------------------------------------------ configure:226781: OMPI configuring in ompi/mca/io/romio/romio configure:226866: running /bin/sh './configure' --with-file-system=testfs+ufs+nfs+lustre FROM_OMPI=yes CC="icc -std=c99" CFLAGS="-DNDEBUG -O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 -m64 -finline-functions -fno-strict-aliasing -restrict -fexceptions -Qoption,cpp,--extended_float_types -pthread" CPPFLAGS=" -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/hwloc/hwloc172/hwloc/include -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent/include" FFLAGS="-O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 -m64 " LDFLAGS="-O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 -m64 -fexceptions " --enable-shared --disable-static --with-file-system=testfs+ufs+nfs+lustre --prefix=/opt/MPI/openmpi-1.8.3/linux/intel --disable-aio --cache-file=/dev/null --srcdir=. --disable-option-checking configure:226876: /bin/sh './configure' *failed* for ompi/mca/io/romio/romio configure:226911: WARNING: ROMIO distribution did not configure successfully configure:227425: checking if MCA component io:romio can compile configure:227427: result: no ------------------------------------------------------------------------------ b) dump of Open MPI's 'configure' output to the console: ------------------------------------------------------------------------------ checking lustre/lustre_user.h usability... no checking lustre/lustre_user.h presence... yes configure: WARNING: lustre/lustre_user.h: present but cannot be compiled configure: WARNING: lustre/lustre_user.h: check for missing prerequisite headers? configure: WARNING: lustre/lustre_user.h: see the Autoconf documentation configure: WARNING: lustre/lustre_user.h: section "Present But Cannot Be Compiled" configure: WARNING: lustre/lustre_user.h: proceeding with the compiler's result configure: WARNING: ## -------------------------------- ## configure: WARNING: ## Report this to discuss(a)mpich.org ## configure: WARNING: ## -------------------------------- ## checking for lustre/lustre_user.h... no configure: error: LUSTRE support requested but cannot find lustre/lustre_user.h header file configure: /bin/sh './configure' *failed* for ompi/mca/io/romio/romio configure: WARNING: ROMIO distribution did not configure successfully checking if MCA component io:romio can compile... no ------------------------------------------------------------------------------ c) ompi/mca/io/romio/romio's config.log: ------------------------------------------------------------------------------ configure:20962: checking lustre/lustre_user.h usability configure:20962: icc -std=c99 -c -DNDEBUG -O3 -ip -axAVX,SSE4.2,SSE4.1 -fp-model fast=2 -m64 -finline-functions -fno-strict-aliasing -restrict -fexceptions -Qoption,cpp,--extended_float_types -pthread -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/hwloc/hwloc172/hwloc/include -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent/include conftest.c >&5 /usr/include/sys/quota.h(221): error: identifier "caddr_t" is undefined caddr_t __addr) __THROW; ^ compilation aborted for conftest.c (code 2) configure:20962: $? = 2 configure: failed program was: | /* confdefs.h */ | #define PACKAGE_NAME "ROMIO" | #define PACKAGE_TARNAME "romio" | #define PACKAGE_VERSION "Open MPI" | #define PACKAGE_STRING "ROMIO Open MPI" | #define PACKAGE_BUGREPORT "discuss(a)mpich.org" | #define PACKAGE_URL "http://www.mpich.org/" | #define PACKAGE "romio" | #define VERSION "Open MPI" | #define STDC_HEADERS 1 | #define HAVE_SYS_TYPES_H 1 | #define HAVE_SYS_STAT_H 1 | #define HAVE_STDLIB_H 1 | #define HAVE_STRING_H 1 | #define HAVE_MEMORY_H 1 | #define HAVE_STRINGS_H 1 | #define HAVE_INTTYPES_H 1 | #define HAVE_STDINT_H 1 | #define HAVE_UNISTD_H 1 | #define HAVE_DLFCN_H 1 | #define LT_OBJDIR ".libs/" | #define HAVE_MPI_OFFSET 1 | #define HAVE_MEMALIGN 1 | #define HAVE_UNISTD_H 1 | #define HAVE_FCNTL_H 1 | #define HAVE_MALLOC_H 1 | #define HAVE_STDDEF_H 1 | #define HAVE_SYS_TYPES_H 1 | #define u_char unsigned char | #define u_short unsigned short | #define u_int unsigned int | #define u_long unsigned long | #define SIZEOF_INT 4 | #define SIZEOF_VOID_P 8 | #define INT_LT_POINTER 1 | #define HAVE_INT_LT_POINTER 1 | #define SIZEOF_LONG_LONG 8 | #define HAVE_LONG_LONG_64 1 | #define HAVE_MPI_LONG_LONG_INT 1 | #define HAVE_MPI_INFO 1 | #define ROMIO_NFS 1 | #define ROMIO_UFS 1 | #define ROMIO_TESTFS 1 | /* end confdefs.h. */ | #include <stdio.h> | #ifdef HAVE_SYS_TYPES_H | # include <sys/types.h> | #endif | #ifdef HAVE_SYS_STAT_H | # include <sys/stat.h> | #endif | #ifdef STDC_HEADERS | # include <stdlib.h> | # include <stddef.h> | #else | # ifdef HAVE_STDLIB_H | # include <stdlib.h> | # endif | #endif | #ifdef HAVE_STRING_H | # if !defined STDC_HEADERS && defined HAVE_MEMORY_H | # include <memory.h> | # endif | # include <string.h> | #endif | #ifdef HAVE_STRINGS_H | # include <strings.h> | #endif | #ifdef HAVE_INTTYPES_H | # include <inttypes.h> | #endif | #ifdef HAVE_STDINT_H | # include <stdint.h> | #endif | #ifdef HAVE_UNISTD_H | # include <unistd.h> | #endif | #include <lustre/lustre_user.h> configure:20962: result: no configure:20962: checking lustre/lustre_user.h presence configure:20962: icc -std=c99 -E -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/hwloc/hwloc172/hwloc/include -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent -I/w0/tmp/pk224850/linuxc2_9713/openmpi-1.8.3_linux64_intel/opal/mca/event/libevent2021/libevent/include conftest.c configure:20962: $? = 0 configure:20962: result: yes configure:20962: WARNING: lustre/lustre_user.h: present but cannot be compiled configure:20962: WARNING: lustre/lustre_user.h: check for missing prerequisite headers? configure:20962: WARNING: lustre/lustre_user.h: see the Autoconf documentation configure:20962: WARNING: lustre/lustre_user.h: section "Present But Cannot Be Compiled" configure:20962: WARNING: lustre/lustre_user.h: proceeding with the compiler's result configure:20962: checking for lustre/lustre_user.h configure:20962: result: no configure:20971: error: LUSTRE support requested but cannot find lustre/lustre_user.h header file ------------------------------------------------------------------------------ -- Dipl.-Inform. Paul Kapinos - High Performance Computing, RWTH Aachen University, IT Center Seffenter Weg 23, D 52074 Aachen (Germany) Tel: +49 241/80-24915 _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re : MPI process killed and SIGUSR1
by Roy, Hirak 27 Oct '14

27 Oct '14

Hi Wesley, This is related to the FT problem. Thanks, Hirak Is this still related to your FT problems or is this a separate problem? Thanks, Wesley _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] buffer overflow
by Md. Amjad Hossain 27 Oct '14

27 Oct '14

Thanks. I found the problem and solved. On Mon, Oct 27, 2014 at 7:49 PM, <discuss-request(a)mpich.org> wrote: > Send discuss mailing list submissions to > discuss(a)mpich.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mpich.org/mailman/listinfo/discuss > or, via email, send a message with subject or body 'help' to > discuss-request(a)mpich.org > > You can reach the person managing the list at > discuss-owner(a)mpich.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of discuss digest..." > > > Today's Topics: > > 1. Re: buffer overflow (Seo, Sangmin) > 2. Re: MPI process killed and SIGUSR1 (Wesley Bland) > 3. Problems in MPICH 3.1.3 installation in OSX 10.10 with ifort > compiler and Xcode 6.1 (Alejandro de la Calle) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 27 Oct 2014 12:52:13 +0000 > From: "Seo, Sangmin" <sseo(a)anl.gov> > To: "<discuss(a)mpich.org>" <discuss(a)mpich.org> > Subject: Re: [mpich-discuss] buffer overflow > Message-ID: <7F837F15-3997-4DD9-9A36-915D94358C95(a)anl.gov> > Content-Type: text/plain; charset="Windows-1252" > > Hi Amjad, > > As the error message, "25 bytes received but buffer size is 24?, says, > your buffer size is smaller than the message size. You need to increase > your buffer which is the memory pointed to by the first argument of > MPI_Recv. > > Best regards, > Sangmin > > > On Oct 27, 2014, at 12:27 AM, Md. Amjad Hossain <mhossai2(a)kent.edu> wrote: > > > Hi, > > > > I am sending and receiving a user defined (struct) data type using > MPI_Send and MPI_Recv function. I am getting following buffer overflow > error. > > > > Fatal error in MPI_Recv: Message truncated, error stack: > > MPI_Recv(187).....................: MPI_Recv(buf=0x7fff2248b930, > count=1, dtype=USER<struct>, src=0, tag=1, MPI_COMM_WORLD, > status=0x7fff2248b970) failed > > MPIDI_CH3U_Receive_data_found(131): Message from rank 0 and tag 1 > truncated; 25 bytes received but buffer size is 24 > > > > > > If I just send one byte less, everything is working properly. Could > anyone please let me know which buffer it is and how can I increase the > buffer size to avoid the error? > > > > Regards > > Amjad > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > ------------------------------ > > Message: 2 > Date: Mon, 27 Oct 2014 09:50:14 -0500 > From: Wesley Bland <wbland(a)anl.gov> > To: "discuss(a)mpich.org" <discuss(a)mpich.org> > Subject: Re: [mpich-discuss] MPI process killed and SIGUSR1 > Message-ID: <1468A5AA-0D18-4ED9-9CEF-4D6625D6564C(a)anl.gov> > Content-Type: text/plain; charset="utf-8" > > Is this still related to your FT problems or is this a separate problem? > > Thanks, > Wesley > > > On Oct 27, 2014, at 6:52 AM, Roy, Hirak <Hirak_Roy(a)mentor.com> wrote: > > > > Hi Wesley, > > > > Here is my server.c and client.c. > > I have explicitly added ?assert(0);? in client.c. > > However my receive hangs in server and does not complete. > > > > Could you please enlighten on this more. > > > > Thanks, > > Hirak > > > > > > #include <sys/types.h> > > #include <unistd.h> > > #include "mpi.h" > > #include <stdio.h> > > #include <assert.h> > > #include <stdlib.h> > > #include <fcntl.h> > > > > > > int main (int argc, char* argv[]) > > { > > > > MPI_Init (&argc, &argv); > > MPI_Errhandler_set(MPI_COMM_WORLD,MPI_ERRORS_RETURN); > > > > char portname[MPI_MAX_PORT_NAME]; > > MPI_Open_port(MPI_INFO_NULL, portname); > > MPI_Publish_name("RandomSession", MPI_INFO_NULL, portname); > > printf ("Successfully published portname : %s\n", portname); > > MPI_Comm newComm ; > > MPI_Comm_accept (portname, MPI_INFO_NULL, 0, MPI_COMM_SELF, &newComm); > > printf ("Successfully connected to client\n"); > > MPI_Errhandler_set(newComm, MPI_ERRORS_RETURN); > > > > printf ("Waiting on receive\n"); > > int val = 0 ; > > MPI_Status status; > > int errcode = MPI_Recv(&val, 1, MPI_INT, 0, 99, newComm, &status); > > int errclass ; > > MPI_Error_class(errcode, &errclass); > > if (errclass == MPI_SUCCESS) { > > printf ("Received a message with tag 99\n"); > > MPI_Comm_disconnect (&newComm); > > printf ("Disconnected client\n"); > > } else { > > printf ("Receive error\n"); > > } > > > > > > MPI_Unpublish_name("RandomSession", MPI_INFO_NULL, portname); > > MPI_Close_port(portname); > > MPI_Finalize(); > > > > } > > > > > > #include <sys/types.h> > > #include <unistd.h> > > #include "mpi.h" > > #include <stdio.h> > > #include <assert.h> > > #include <stdlib.h> > > #include <fcntl.h> > > > > > > int main (int argc, char* argv[]) > > { > > MPI_Init (&argc, &argv); > > MPI_Errhandler_set(MPI_COMM_WORLD,MPI_ERRORS_RETURN); > > > > char portname[MPI_MAX_PORT_NAME]; > > if (MPI_Lookup_name("RandomSession", MPI_INFO_NULL, portname) == > MPI_SUCCESS) { > > printf ("Successfully got portname : %s\n", portname); > > MPI_Comm newComm ; > > MPI_Comm_connect (portname, MPI_INFO_NULL, 0, MPI_COMM_SELF, > &newComm); > > printf ("Successfully connected to server\n"); > > MPI_Errhandler_set(newComm, MPI_ERRORS_RETURN); > > > > assert (0); > > int val = 0 ; > > MPI_Send(&val, 1, MPI_INT, 0, 99, newComm); > > printf ("Send a message with tag 99\n"); > > MPI_Comm_disconnect (&newComm); > > printf ("Disconnected client\n"); > > } > > MPI_Finalize(); > > } > > MPICH Version: 3.0.4 > > MPICH Release date: Wed Apr 24 10:08:10 CDT 2013 > > MPICH Device: ch3:sock > > MPICH configure: --prefix > /home/jlevitt/local/mpich-3.0.4/linux_x86_64 --disable-f77 --disable-fc > --disable-f90modules --disable-cxx --enable-fast=nochkmsg > --enable-fast=notiming --enable-fast=ndebug --enable-fast=O3 > --with-device=ch3:sock CFLAGS=-O3 -fPIC CXXFLAGS=-O3 -fPIC > > MPICH CC: /u/prod/gnu/gcc/20121129/gcc-4.5.0-linux_x86_64/bin/gcc -O3 > -fPIC -O3 > > MPICH CXX: no -O3 -fPIC > > MPICH F77: no > > MPICH FC: no > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss < > https://lists.mpich.org/mailman/listinfo/discuss> > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Problems in MPICH 3.1.3 installation in OSX 10.10 with ifort compiler and Xcode 6.1
by Alejandro de la Calle 27 Oct '14

27 Oct '14

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Re: [mpich-discuss] MPI process killed and SIGUSR1
by Wesley Bland 27 Oct '14

27 Oct '14

Is this still related to your FT problems or is this a separate problem? Thanks, Wesley > On Oct 27, 2014, at 6:52 AM, Roy, Hirak <Hirak_Roy(a)mentor.com> wrote: > > Hi Wesley, > > Here is my server.c and client.c. > I have explicitly added ‘assert(0);’ in client.c. > However my receive hangs in server and does not complete. > > Could you please enlighten on this more. > > Thanks, > Hirak > > > #include <sys/types.h> > #include <unistd.h> > #include "mpi.h" > #include <stdio.h> > #include <assert.h> > #include <stdlib.h> > #include <fcntl.h> > > > int main (int argc, char* argv[]) > { > > MPI_Init (&argc, &argv); > MPI_Errhandler_set(MPI_COMM_WORLD,MPI_ERRORS_RETURN); > > char portname[MPI_MAX_PORT_NAME]; > MPI_Open_port(MPI_INFO_NULL, portname); > MPI_Publish_name("RandomSession", MPI_INFO_NULL, portname); > printf ("Successfully published portname : %s\n", portname); > MPI_Comm newComm ; > MPI_Comm_accept (portname, MPI_INFO_NULL, 0, MPI_COMM_SELF, &newComm); > printf ("Successfully connected to client\n"); > MPI_Errhandler_set(newComm, MPI_ERRORS_RETURN); > > printf ("Waiting on receive\n"); > int val = 0 ; > MPI_Status status; > int errcode = MPI_Recv(&val, 1, MPI_INT, 0, 99, newComm, &status); > int errclass ; > MPI_Error_class(errcode, &errclass); > if (errclass == MPI_SUCCESS) { > printf ("Received a message with tag 99\n"); > MPI_Comm_disconnect (&newComm); > printf ("Disconnected client\n"); > } else { > printf ("Receive error\n"); > } > > > MPI_Unpublish_name("RandomSession", MPI_INFO_NULL, portname); > MPI_Close_port(portname); > MPI_Finalize(); > > } > > > #include <sys/types.h> > #include <unistd.h> > #include "mpi.h" > #include <stdio.h> > #include <assert.h> > #include <stdlib.h> > #include <fcntl.h> > > > int main (int argc, char* argv[]) > { > MPI_Init (&argc, &argv); > MPI_Errhandler_set(MPI_COMM_WORLD,MPI_ERRORS_RETURN); > > char portname[MPI_MAX_PORT_NAME]; > if (MPI_Lookup_name("RandomSession", MPI_INFO_NULL, portname) == MPI_SUCCESS) { > printf ("Successfully got portname : %s\n", portname); > MPI_Comm newComm ; > MPI_Comm_connect (portname, MPI_INFO_NULL, 0, MPI_COMM_SELF, &newComm); > printf ("Successfully connected to server\n"); > MPI_Errhandler_set(newComm, MPI_ERRORS_RETURN); > > assert (0); > int val = 0 ; > MPI_Send(&val, 1, MPI_INT, 0, 99, newComm); > printf ("Send a message with tag 99\n"); > MPI_Comm_disconnect (&newComm); > printf ("Disconnected client\n"); > } > MPI_Finalize(); > } > MPICH Version: 3.0.4 > MPICH Release date: Wed Apr 24 10:08:10 CDT 2013 > MPICH Device: ch3:sock > MPICH configure: --prefix /home/jlevitt/local/mpich-3.0.4/linux_x86_64 --disable-f77 --disable-fc --disable-f90modules --disable-cxx --enable-fast=nochkmsg --enable-fast=notiming --enable-fast=ndebug --enable-fast=O3 --with-device=ch3:sock CFLAGS=-O3 -fPIC CXXFLAGS=-O3 -fPIC > MPICH CC: /u/prod/gnu/gcc/20121129/gcc-4.5.0-linux_x86_64/bin/gcc -O3 -fPIC -O3 > MPICH CXX: no -O3 -fPIC > MPICH F77: no > MPICH FC: no > _______________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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