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

Re: [mpich-discuss] Build Problem mpich-3.1.3
by Seo, Sangmin 31 Oct '14

31 Oct '14

Hi Hirak, Can you send us c.txt as described in http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3-installguide.pdf? In the meantime, you can also try configure with '--without-valgrind’. I think it can be a problem of valgrind version. Regards, Sangmin On Oct 31, 2014, at 5:44 AM, Hirak Roy <hirak_roy(a)mentor.com<mailto:[email protected]>> wrote: Hi Team, I could not complete the build. Could you please let me know if it is config issue or anything else. Thanks, Hirak make all-recursive make[1]: Entering directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3' Making all in /net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3/src/mpl make[2]: Entering directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3/src/mpl' CC src/mpltrmem.lo src/mpltrmem.c: In function 'MPL_trdump': src/mpltrmem.c:657:9: error: 'old_head' undeclared (first use in this function) src/mpltrmem.c:657:9: note: each undeclared identifier is reported only once for each function it appears in make[2]: *** [src/mpltrmem.lo] Error 1 make[2]: Leaving directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3/src/mpl' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3' make: *** [all] Error 2 My linux distribution : Linux zinblade62 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44 EST 2007 x86_64 x86_64 x86_64 GNU/Linux Config settings: Configuring with : mpich2 version = 3.1.3 platform = linux_x86_64 Source directory = /net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3 Install directory = /home/hroy/local//mpich-3.1.3/linux_x86_64 CC = /u/prod/gnu/gcc/20121129/gcc-4.5.0-linux_x86_64/bin/gcc CFLAGS = -O3 -fPIC CXXFLAGS = -O3 -fPIC LDFLAGS = CONFIG_OPTIONS = --disable-f77 --disable-fc --disable-f90modules --disable-cxx --enable-fast=nochkmsg --enable-fast=notiming --enable-fast=ndebug --enable-fast=O3 --with-device=ch3:sock --enable-g=dbg --disable-fortran _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> 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] Problem with RMA && MPI_Type_vector when stride value is relatively large (UPD)
by Zhao, Xin 31 Oct '14

31 Oct '14

Hi Victor, The "at_completion_counter" is used to detect the completion of all RMA operations on target side, (Win_fence / Win_complete can return after it reaches zero). It is initialized as the number of expected origins and is decremented when target receives the last operation from one origin. However, the GET-like operations needs to send back data, which may not finish immediately when target receives the GET-like packet, so here we increment that counter when target receives a GET-like packet and decrement it when the sending back process finishes (where your assertion failure happens). Is it possible for you to reproduce this bug in a simple program? So that I can look at what's going wrong. Thanks, Xin ________________________________________ From: Victor Vysotskiy [victor.vysotskiy(a)teokem.lu.se] Sent: Friday, October 31, 2014 5:47 AM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Problem with RMA && MPI_Type_vector when stride value is relatively large (UPD) Dear Xin, thank you very much for your efforts! Indeed, the test-bed code works out within your recent fix. However, my real application now is failing with the following error message: Assertion failed in file src/mpid/ch3/src/ch3u_handle_send_req.c at line 61: win_ptr->at_completion_counter >= 0 internal ABORT - process 10 Do you, by any chance, have any idea what might cause such error? Could you please advise me how to debug this problem? With best regards, Victor. _______________________________________________ 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] Problem with RMA && MPI_Type_vector when stride value is relatively large (UPD)
by Victor Vysotskiy 31 Oct '14

31 Oct '14

Dear Xin, thank you very much for your efforts! Indeed, the test-bed code works out within your recent fix. However, my real application now is failing with the following error message: Assertion failed in file src/mpid/ch3/src/ch3u_handle_send_req.c at line 61: win_ptr->at_completion_counter >= 0 internal ABORT - process 10 Do you, by any chance, have any idea what might cause such error? Could you please advise me how to debug this problem? With best regards, Victor. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Build Problem mpich-3.1.3
by Hirak Roy 31 Oct '14

31 Oct '14

Hi Team, I could not complete the build. Could you please let me know if it is config issue or anything else. Thanks, Hirak make all-recursive make[1]: Entering directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3' Making all in /net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3/src/mpl make[2]: Entering directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3/src/mpl' CC src/mpltrmem.lo src/mpltrmem.c: In function 'MPL_trdump': src/mpltrmem.c:657:9: error: 'old_head' undeclared (first use in this function) src/mpltrmem.c:657:9: note: each undeclared identifier is reported only once for each function it appears in make[2]: *** [src/mpltrmem.lo] Error 1 make[2]: Leaving directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3/src/mpl' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3' make: *** [all] Error 2 My linux distribution : Linux zinblade62 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:56:44 EST 2007 x86_64 x86_64 x86_64 GNU/Linux Config settings: Configuring with : mpich2 version = 3.1.3 platform = linux_x86_64 Source directory = /net/zinzeng17/export/hroy/software/MPI/mpich-3.1.3 Install directory = /home/hroy/local//mpich-3.1.3/linux_x86_64 CC = /u/prod/gnu/gcc/20121129/gcc-4.5.0-linux_x86_64/bin/gcc CFLAGS = -O3 -fPIC CXXFLAGS = -O3 -fPIC LDFLAGS = CONFIG_OPTIONS = --disable-f77 --disable-fc --disable-f90modules --disable-cxx --enable-fast=nochkmsg --enable-fast=notiming --enable-fast=ndebug --enable-fast=O3 --with-device=ch3:sock --enable-g=dbg --disable-fortran _______________________________________________ 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] Problem with RMA && MPI_Type_vector when stride value is relatively large (UPD)
by Zhao, Xin 30 Oct '14

30 Oct '14

Hi Victor, The bug is recently fixed: https://trac.mpich.org/projects/mpich/ticket/2189 You can try tonight's mpich nightly snapshot, which will be available from http://www.mpich.org/static/downloads/nightly/master/mpich/ Thanks, Xin ________________________________ From: Zhao, Xin Sent: Thursday, October 16, 2014 12:59 PM To: discuss(a)mpich.org Subject: RE: [mpich-discuss] Problem with RMA && MPI_Type_vector when stride value is relatively large (UPD) Hi Victor, I think it is due to a bug for MPI_PUT to handle large derived datatype and we will fix it as soon as possible. The code works with MPI_GET. You can track this bug at: https://trac.mpich.org/projects/mpich/ticket/2189 Thanks, Xin ________________________________ From: Victor Vysotskiy [victor.vysotskiy(a)teokem.lu.se] Sent: Thursday, October 16, 2014 11:19 AM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Problem with RMA && MPI_Type_vector when stride value is relatively large (UPD) Hi, I am sorry that the test bed code has not been attached to the original message. Enclosed please find it. I have also checked the issue in MPICH v3.1.3. Unfortunately, the latest MPICH3 version behaves exactly the same as the MPICH2 v1.5, i.e. it also hangs at "30000 2000". With best regards, Victor. P.s. Below is given an update on MPICH3 version used: MPICH2 Version: 3.1.3 MPICH2 Release date: Wed Oct 8 09:37:19 CDT 2014 MPICH2 Device: ch3:nemesis MPICH2 configure: --prefix=/opt/mpi/mpich3-1.3/ --disable-weak-symbols MPICH2 CC: gcc -O2 MPICH2 CXX: c++ -O2 MPICH2 F77: gfortran -O2 MPICH2 FC: gfortran -O2 GCC version 4.7.3 ________________________________ From: Victor Vysotskiy Sent: Thursday, October 16, 2014 1:34 PM To: discuss(a)mpich.org Subject: Problem with RMA && MPI_Type_vector when stride value is relatively large Hi, I am straggling with a simple MPI program when a vector derived datatype is used as origin/remote datatypes in the MPI_Put RMA operation. The underlying idea is quite simple: a contiguous piece of memory is interpreted as a 2D array and only its certain slice is going to be updated via MPI_Put. To this end, I am using a MPI_Type_vector call. Everything works fine when the stride value <= 24000, regardless count and blocklength. However, if stride is greater than 24000 then program simply hangs. The source code is attached and you can simply verify the issue by compiling and running it with the following parameters: mpicc mpi_tvec_rma.c mpirun -np 2 ./a.out 10000 2000 Ok mpirun -np 2 ./a.out 20000 2000 Ok mpirun -np 2 ./a.out 30000 2000 Hangs Is there any internal/known limits to the size of MPI_TYPE_VECTOR datatypes? So, I am really puzzled what is happening here and any help will be greatly appreciated! With best regards, Victor. P.S. The attached code is perfectly runs with the OpenMPI v1.8.2. P.P.S. Below are given some details about hardware and software setups used: MPICH2 Version: 1.5 MPICH2 Release date: Mon Oct 8 14:00:48 CDT 2012 MPICH2 Device: ch3:nemesis MPICH2 configure: --prefix=/opt/mpi/mpich2/ --disable-weak-symbols MPICH2 CC: gcc -O2 MPICH2 CXX: c++ -O2 MPICH2 F77: gfortran -O2 MPICH2 FC: gfortran -O2 GCC version 4.7.3 _______________________________________________ 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] [OMPI devel] ROMIO+Lustre problems in OpenMPI 1.8.3
by Paul Kapinos 30 Oct '14

30 Oct '14

(2nd try as the first log package was too big) Hello Howard, The version 1.8.1 installed on Jun 27 this year run fine, ROMIO is OK. Trying ro re-run using the same install script: found out that also 1.8.1 version of Open MPI now *cannot* build ROMIO support. Wow. That means that the regression is not/not only in the OpenMPI's ROMIO, but depends on our Linux/Kernel/Lustre. Very first look: we've new kernel and new /usr/include/sys/quota.h and we probably update from SL6.4 to SL6.5. - which information about our Linux/System do you need? - Interest/Need in getting a guest login to get in-deepth feeling? Best Paul Kapinos Attached: some logs from Instalation at 27.05 and today't try, and quota.h (changed at 29.09). Note that also the kernel changed (and maybe the Scientific Linux version from 6.4 to 6.5?) pk224850@cluster:~[502]$ ls -la /usr/include/sys/quota.h -rw-r--r-- 1 root root 7903 Aug 29 21:11 /usr/include/sys/quota.h pk224850@cluster:~[503]$ 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:~[504]$ cat /etc/issue Scientific Linux release 6.5 (Carbon) Kernel \r on an \m On 10/29/14 19:06, Howard Pritchard wrote: > Hi Paul, > > Thanks for the forward. I've opened an issue #255 > <https://github.com/open-mpi/ompi/issues/255> to track the ROMIO config regression. > > Just to make sure, older releases of the 1.8 branch still configure and build > properly with your > current lustre setup? > > Thanks, > > Howard > > > 2014-10-28 5:00 GMT-06:00 Paul Kapinos <kapinos(a)itc.rwth-aachen.de > <mailto:[email protected]>>: > > 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 <http://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 > <mailto:[email protected]> ## > 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 <mailto:[email protected]>" > | #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 <tel:%2B49%20241%2F80-24915> > > _______________________________________________ > devel mailing list > devel(a)open-mpi.org <mailto:[email protected]> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel > Link to this post: > http://www.open-mpi.org/community/lists/devel/2014/10/16106.php > > > > > _______________________________________________ > devel mailing list > devel(a)open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel > Link to this post: http://www.open-mpi.org/community/lists/devel/2014/10/16127.php > -- 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: [mpich-discuss] [OMPI devel] ROMIO+Lustre problems in OpenMPI 1.8.3
by Paul Kapinos 30 Oct '14

30 Oct '14

Hello Howard, The version 1.8.1 installed on Jun 27 this year run fine, ROMIO is OK. Trying ro re-run using the same install script: found out that also 1.8.1 version of Open MPI now *cannot* build ROMIO support. Wow. That means that the regression is not/not only in the OpenMPI's ROMIO, but depends on our Linux/Kernel/Lustre. Very first look: we've new kernel and new /usr/include/sys/quota.h and we probably update from SL6.4 to SL6.5. - which information about our Linux/System do you need? - Interest/Need in getting a guest login to get in-deepth feeling? Best Paul Kapinos Attached: some logs from Instalation at 27.05 and today't try, and quota.h (changed at 29.09). Note that also the kernel changed (and maybe the Scientific Linux version from 6.4 to 6.5?) pk224850@cluster:~[502]$ ls -la /usr/include/sys/quota.h -rw-r--r-- 1 root root 7903 Aug 29 21:11 /usr/include/sys/quota.h pk224850@cluster:~[503]$ 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:~[504]$ cat /etc/issue Scientific Linux release 6.5 (Carbon) Kernel \r on an \m On 10/29/14 19:06, Howard Pritchard wrote: > Hi Paul, > > Thanks for the forward. I've opened an issue #255 > <https://github.com/open-mpi/ompi/issues/255> to track the ROMIO config regression. > > Just to make sure, older releases of the 1.8 branch still configure and build > properly with your > current lustre setup? > > Thanks, > > Howard > > > 2014-10-28 5:00 GMT-06:00 Paul Kapinos <kapinos(a)itc.rwth-aachen.de > <mailto:[email protected]>>: > > 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 <http://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 > <mailto:[email protected]> ## > 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 <mailto:[email protected]>" > | #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 <tel:%2B49%20241%2F80-24915> > > _______________________________________________ > devel mailing list > devel(a)open-mpi.org <mailto:[email protected]> > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel > Link to this post: > http://www.open-mpi.org/community/lists/devel/2014/10/16106.php > > > > > _______________________________________________ > devel mailing list > devel(a)open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel > Link to this post: http://www.open-mpi.org/community/lists/devel/2014/10/16127.php > -- 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

1 0

Re: [mpich-discuss] trouble installing
by Wesley Bland 30 Oct '14

30 Oct '14

You can also avoid most of the installation nastiness by just use Homebrew for your installation. That’s our officially supported method for OSX. The Macports guys also have MPICH available through their package manager. Thanks, Wesley > On Oct 30, 2014, at 8:29 AM, Lu, Huiwei <huiweilu(a)mcs.anl.gov> wrote: > > Thanks for reporting your install information. Looks like the configure didn’t detect your environment correctly. It should detect that you did not have fortran installed and should not check fortran bindings afterwards. > > Before we fix the configure, would you like to try the following first: if you do not need fortran, you can configure MPICH with ‘configure --disable-fortran’. If you need fortran, please install fortran compiler and try again. > > p.s. Michael: we are using discuss(a)mpich.org instead of mpich-discuss(a)mcs.anl.gov now. > — > Huiwei > >> On Oct 29, 2014, at 11:50 PM, Michael Steffen <michael-steffen(a)utulsa.edu> wrote: >> >> I am having trouble installing mpich on my macbook pro. >> >> This is what my terminal window looks like when I try to install it at get stuck at the make part. >> >> What am I doing wrong? >> >> Last login: Wed Oct 29 22:36:42 on ttys000 >> Michaels-MacBook-Pro:~ michael-steffen$ cd /Users/michael-steffen/Desktop/mpich-3.1.3 >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ /Users/michael-steffen/Desktop/mpich-3.1.3/configure >> Configuring MPICH version 3.1.3 >> Running on system: Darwin Michaels-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 >> checking for icc... no >> checking for pgcc... no >> checking for xlc... no >> checking for xlC... no >> checking for pathcc... no >> checking for gcc... gcc >> checking whether the C compiler works... yes >> checking for C compiler default output file name... a.out >> checking for suffix of executables... >> checking whether we are cross compiling... no >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking whether gcc understands -c and -o together... yes >> checking how to run the C preprocessor... gcc -E >> checking for a BSD-compatible install... /usr/bin/install -c >> checking whether build environment is sane... yes >> checking for a thread-safe mkdir -p... confdb/install-sh -c -d >> checking for gawk... no >> checking for mawk... no >> checking for nawk... no >> checking for awk... awk >> checking whether make sets $(MAKE)... yes >> checking for style of include used by make... GNU >> checking whether make supports nested variables... yes >> checking dependency style of gcc... gcc3 >> checking whether to enable maintainer-specific portions of Makefiles... yes >> checking for ar... ar >> checking the archiver (ar) interface... ar >> checking build system type... x86_64-apple-darwin13.4.0 >> checking host system type... x86_64-apple-darwin13.4.0 >> checking how to print strings... printf >> checking for a sed that does not truncate output... /usr/bin/sed >> checking for grep that handles long lines and -e... /usr/bin/grep >> checking for egrep... /usr/bin/grep -E >> checking for fgrep... /usr/bin/grep -F >> checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld >> checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no >> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm >> checking the name lister (/usr/bin/nm) interface... BSD nm >> checking whether ln -s works... yes >> checking the maximum length of command line arguments... 196608 >> checking whether the shell understands some XSI constructs... yes >> checking whether the shell understands "+="... yes >> checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop >> checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop >> checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r >> checking for objdump... no >> checking how to recognize dependent libraries... pass_all >> checking for dlltool... no >> checking how to associate runtime and link libraries... printf %s\n >> checking for archiver @FILE support... no >> checking for strip... strip >> checking for ranlib... ranlib >> checking command to parse /usr/bin/nm output from gcc object... ok >> checking for sysroot... no >> checking for mt... no >> checking if : is a manifest tool... no >> checking for dsymutil... dsymutil >> checking for nmedit... nmedit >> checking for lipo... lipo >> checking for otool... otool >> checking for otool64... no >> checking for -single_module linker flag... yes >> checking for -exported_symbols_list linker flag... yes >> checking for -force_load linker flag... yes >> checking for ANSI C header files... yes >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking for dlfcn.h... yes >> checking for objdir... .libs >> checking if gcc supports -fno-rtti -fno-exceptions... yes >> checking for gcc option to produce PIC... -fno-common -DPIC >> checking if gcc PIC flag -fno-common -DPIC works... yes >> checking if gcc static flag -static works... no >> checking if gcc supports -c -o file.o... yes >> checking if gcc supports -c -o file.o... (cached) yes >> checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes >> checking dynamic linker characteristics... darwin13.4.0 dyld >> checking how to hardcode library paths into programs... immediate >> checking whether stripping libraries is possible... yes >> checking if libtool supports shared libraries... yes >> checking whether to build shared libraries... yes >> checking whether to build static libraries... yes >> checking whether make supports nested variables... (cached) yes >> checking for icpc... no >> checking for pgCC... no >> checking for xlC... no >> checking for pathCC... no >> checking for g++... g++ >> checking whether we are using the GNU C++ compiler... yes >> checking whether g++ accepts -g... yes >> checking dependency style of g++... gcc3 >> checking how to run the C++ preprocessor... g++ -E >> checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld >> checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no >> checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes >> checking for g++ option to produce PIC... -fno-common -DPIC >> checking if g++ PIC flag -fno-common -DPIC works... yes >> checking if g++ static flag -static works... no >> checking if g++ supports -c -o file.o... yes >> checking if g++ supports -c -o file.o... (cached) yes >> checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes >> checking dynamic linker characteristics... darwin13.4.0 dyld >> checking how to hardcode library paths into programs... immediate >> checking for ifort... no >> checking for pgf90... no >> checking for pathf90... no >> checking for pathf95... no >> checking for xlf90... no >> checking for xlf95... no >> checking for xlf2003... no >> checking for gfortran... no >> checking for f90... no >> checking for epcf90... no >> checking for f95... no >> checking for fort... no >> checking for lf95... no >> checking for g95... no >> checking for ifc... no >> checking for efc... no >> checking for gfc... no >> checking whether we are using the GNU Fortran compiler... no >> checking whether accepts -g... no >> checking for ifort... no >> checking for pgf77... no >> checking for af77... no >> checking for xlf... no >> checking for frt... no >> checking for cf77... no >> checking for fort77... no >> checking for fl32... no >> checking for fort... no >> checking for ifc... no >> checking for efc... no >> checking for ftn... no >> checking for gfortran... no >> checking for f77... no >> checking for g77... no >> checking whether we are using the GNU Fortran 77 compiler... no >> checking whether accepts -g... no >> checking hcoll/api/hcoll_api.h usability... no >> checking hcoll/api/hcoll_api.h presence... no >> checking for hcoll/api/hcoll_api.h... no >> checking for hcoll_init in -lhcoll... no >> configure: RUNNING PREREQ FOR ch3:nemesis >> checking for getpagesize... yes >> checking for getpagesize... (cached) yes >> configure: ===== configuring src/mpl ===== >> configure: running /bin/sh ./configure --disable-option-checking '--prefix=NONE' --cache-file=/dev/null --srcdir=. >> checking for a BSD-compatible install... /usr/bin/install -c >> checking whether build environment is sane... yes >> checking for a thread-safe mkdir -p... confdb/install-sh -c -d >> checking for gawk... no >> checking for mawk... no >> checking for nawk... no >> checking for awk... awk >> checking whether make sets $(MAKE)... yes >> checking whether make supports nested variables... yes >> checking for style of include used by make... GNU >> checking whether the C compiler works... yes >> checking for C compiler default output file name... a.out >> checking for suffix of executables... >> checking whether we are cross compiling... no >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking whether gcc understands -c and -o together... yes >> checking dependency style of gcc... gcc3 >> checking the archiver (ar) interface... ar >> checking build system type... x86_64-apple-darwin13.4.0 >> checking host system type... x86_64-apple-darwin13.4.0 >> checking how to print strings... printf >> checking for a sed that does not truncate output... /usr/bin/sed >> checking for grep that handles long lines and -e... /usr/bin/grep >> checking for egrep... /usr/bin/grep -E >> checking for fgrep... /usr/bin/grep -F >> checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld >> checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no >> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm >> checking the name lister (/usr/bin/nm) interface... BSD nm >> checking whether ln -s works... yes >> checking the maximum length of command line arguments... 196608 >> checking whether the shell understands some XSI constructs... yes >> checking whether the shell understands "+="... yes >> checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop >> checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop >> checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r >> checking for objdump... no >> checking how to recognize dependent libraries... pass_all >> checking for dlltool... no >> checking how to associate runtime and link libraries... printf %s\n >> checking for archiver @FILE support... no >> checking for strip... strip >> checking for ranlib... ranlib >> checking command to parse /usr/bin/nm output from gcc object... ok >> checking for sysroot... no >> checking for mt... no >> checking if : is a manifest tool... no >> checking for dsymutil... dsymutil >> checking for nmedit... nmedit >> checking for lipo... lipo >> checking for otool... otool >> checking for otool64... no >> checking for -single_module linker flag... yes >> checking for -exported_symbols_list linker flag... yes >> checking for -force_load linker flag... yes >> checking how to run the C preprocessor... gcc -E >> checking for ANSI C header files... yes >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking for dlfcn.h... yes >> checking for objdir... .libs >> checking if gcc supports -fno-rtti -fno-exceptions... yes >> checking for gcc option to produce PIC... -fno-common -DPIC >> checking if gcc PIC flag -fno-common -DPIC works... yes >> checking if gcc static flag -static works... no >> checking if gcc supports -c -o file.o... yes >> checking if gcc supports -c -o file.o... (cached) yes >> checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes >> checking dynamic linker characteristics... darwin13.4.0 dyld >> checking how to hardcode library paths into programs... immediate >> checking whether stripping libraries is possible... yes >> checking if libtool supports shared libraries... yes >> checking whether to build shared libraries... yes >> checking whether to build static libraries... yes >> checking whether make supports nested variables... (cached) yes >> checking for an ANSI C-conforming const... yes >> checking for C/C++ restrict keyword... __restrict >> checking for inline... inline >> checking for variable argument list macro functionality... yes >> checking for gcov... gcov >> checking whether the compiler supports __typeof(variable)... yes >> checking stdio.h usability... yes >> checking stdio.h presence... yes >> checking for stdio.h... yes >> checking for stdlib.h... (cached) yes >> checking for string.h... (cached) yes >> checking stdarg.h usability... yes >> checking stdarg.h presence... yes >> checking for stdarg.h... yes >> checking ctype.h usability... yes >> checking ctype.h presence... yes >> checking for ctype.h... yes >> checking search.h usability... yes >> checking search.h presence... yes >> checking for search.h... yes >> checking for sys/types.h... (cached) yes >> checking sys/uio.h usability... yes >> checking sys/uio.h presence... yes >> checking for sys/uio.h... yes >> checking for inttypes.h... (cached) yes >> checking for stdint.h... (cached) yes >> checking valgrind.h usability... no >> checking valgrind.h presence... no >> checking for valgrind.h... no >> checking memcheck.h usability... no >> checking memcheck.h presence... no >> checking for memcheck.h... no >> checking valgrind/valgrind.h usability... no >> checking valgrind/valgrind.h presence... no >> checking for valgrind/valgrind.h... no >> checking valgrind/memcheck.h usability... no >> checking valgrind/memcheck.h presence... no >> checking for valgrind/memcheck.h... no >> checking helgrind.h usability... no >> checking helgrind.h presence... no >> checking for helgrind.h... no >> checking valgrind/helgrind.h usability... no >> checking valgrind/helgrind.h presence... no >> checking for valgrind/helgrind.h... no >> checking drd.h usability... no >> checking drd.h presence... no >> checking for drd.h... no >> checking valgrind/drd.h usability... no >> checking valgrind/drd.h presence... no >> checking for valgrind/drd.h... no >> checking whether the valgrind headers are broken or too old... yes >> checking for strdup... yes >> checking whether strdup needs a declaration... no >> checking for snprintf... yes >> checking whether snprintf needs a declaration... no >> checking for strncmp... yes >> checking whether strncmp needs a declaration... no >> checking for putenv... yes >> checking whether putenv needs a declaration... no >> checking whether __attribute__ allowed... yes >> checking whether __attribute__((format)) allowed... yes >> checking that generated files are newer than configure... done >> configure: creating ./config.status >> config.status: creating Makefile >> config.status: creating localdefs >> config.status: creating include/config.h >> config.status: executing depfiles commands >> config.status: executing libtool commands >> config.status: executing include/mplconfig.h commands >> config.status: creating include/mplconfig.h - prefix MPL for include/config.h defines >> configure: ===== done with src/mpl configure ===== >> configure: sourcing src/mpl/localdefs >> configure: ===== configuring src/openpa ===== >> configure: running /bin/sh ./configure --disable-option-checking '--prefix=NONE' --with-atomic-primitives=auto_allow_emulation --cache-file=/dev/null --srcdir=. >> checking for a BSD-compatible install... /usr/bin/install -c >> checking whether build environment is sane... yes >> checking for a thread-safe mkdir -p... confdb/install-sh -c -d >> checking for gawk... no >> checking for mawk... no >> checking for nawk... no >> checking for awk... awk >> checking whether make sets $(MAKE)... yes >> checking whether make supports nested variables... yes >> checking for style of include used by make... GNU >> checking for gcc... gcc >> checking whether the C compiler works... yes >> checking for C compiler default output file name... a.out >> checking for suffix of executables... >> checking whether we are cross compiling... no >> checking for suffix of object files... o >> checking whether we are using the GNU C compiler... yes >> checking whether gcc accepts -g... yes >> checking for gcc option to accept ISO C89... none needed >> checking whether gcc understands -c and -o together... yes >> checking dependency style of gcc... gcc3 >> checking the archiver (ar) interface... ar >> checking build system type... x86_64-apple-darwin13.4.0 >> checking host system type... x86_64-apple-darwin13.4.0 >> checking how to print strings... printf >> checking for a sed that does not truncate output... /usr/bin/sed >> checking for grep that handles long lines and -e... /usr/bin/grep >> checking for egrep... /usr/bin/grep -E >> checking for fgrep... /usr/bin/grep -F >> checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld >> checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no >> checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm >> checking the name lister (/usr/bin/nm) interface... BSD nm >> checking whether ln -s works... yes >> checking the maximum length of command line arguments... 196608 >> checking whether the shell understands some XSI constructs... yes >> checking whether the shell understands "+="... yes >> checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop >> checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop >> checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r >> checking for objdump... no >> checking how to recognize dependent libraries... pass_all >> checking for dlltool... no >> checking how to associate runtime and link libraries... printf %s\n >> checking for archiver @FILE support... no >> checking for strip... strip >> checking for ranlib... ranlib >> checking command to parse /usr/bin/nm output from gcc object... ok >> checking for sysroot... no >> checking for mt... no >> checking if : is a manifest tool... no >> checking for dsymutil... dsymutil >> checking for nmedit... nmedit >> checking for lipo... lipo >> checking for otool... otool >> checking for otool64... no >> checking for -single_module linker flag... yes >> checking for -exported_symbols_list linker flag... yes >> checking for -force_load linker flag... yes >> checking how to run the C preprocessor... gcc -E >> checking for ANSI C header files... yes >> checking for sys/types.h... yes >> checking for sys/stat.h... yes >> checking for stdlib.h... yes >> checking for string.h... yes >> checking for memory.h... yes >> checking for strings.h... yes >> checking for inttypes.h... yes >> checking for stdint.h... yes >> checking for unistd.h... yes >> checking for dlfcn.h... yes >> checking for objdir... .libs >> checking if gcc supports -fno-rtti -fno-exceptions... yes >> checking for gcc option to produce PIC... -fno-common -DPIC >> checking if gcc PIC flag -fno-common -DPIC works... yes >> checking if gcc static flag -static works... no >> checking if gcc supports -c -o file.o... yes >> checking if gcc supports -c -o file.o... (cached) yes >> checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes >> checking dynamic linker characteristics... darwin13.4.0 dyld >> checking how to hardcode library paths into programs... immediate >> checking whether stripping libraries is possible... yes >> checking if libtool supports shared libraries... yes >> checking whether to build shared libraries... yes >> checking whether to build static libraries... yes >> checking whether make supports nested variables... (cached) yes >> checking for gcc... (cached) gcc >> checking whether we are using the GNU C compiler... (cached) yes >> checking whether gcc accepts -g... (cached) yes >> checking for gcc option to accept ISO C89... (cached) none needed >> checking whether gcc understands -c and -o together... (cached) yes >> checking dependency style of gcc... (cached) gcc3 >> checking whether to enable assertions... yes >> checking pthread.h usability... yes >> checking pthread.h presence... yes >> checking for pthread.h... yes >> checking atomic.h usability... no >> checking atomic.h presence... no >> checking for atomic.h... no >> checking intrin.h usability... no >> checking intrin.h presence... no >> checking for intrin.h... no >> checking for inttypes.h... (cached) yes >> checking for stdint.h... (cached) yes >> checking stddef.h usability... yes >> checking stddef.h presence... yes >> checking for stddef.h... yes >> checking for C/C++ restrict keyword... __restrict >> checking for inline... inline >> checking for an ANSI C-conforming const... yes >> checking for pthread_create in -lpthread... yes >> checking for pthread_yield... no >> checking sched.h usability... yes >> checking sched.h presence... yes >> checking for sched.h... yes >> checking for sched_yield... yes >> checking if 100 threads can be run at once... yes >> checking size of void *... 8 >> checking size of int... 4 >> checking whether __attribute__ allowed... yes >> checking whether __attribute__((format)) allowed... yes >> checking if compiler rejects bogus asm statements... yes >> checking for support for gcc x86/x86_64 primitives... yes >> checking for support for gcc x86 primitives for pre-Pentium 4... yes >> checking for support for gcc ia64 primitives... no >> checking for support for gcc PowerPC atomics... no >> checking for support for gcc ARM atomics... no >> checking for support for gcc SiCortex atomics... no >> checking for support for gcc atomic intrinsics... yes >> checking for support for Windows NT atomic intrinsics... no >> checking for support for Sun atomic operations library... no >> checking whether to enable strict fairness checks... no >> checking that generated files are newer than configure... done >> configure: creating ./config.status >> config.status: creating Makefile >> config.status: creating src/Makefile >> config.status: creating test/Makefile >> config.status: creating openpa.pc >> config.status: creating src/config.h >> config.status: executing depfiles commands >> config.status: executing libtool commands >> config.status: executing src/opa_config.h commands >> config.status: creating src/opa_config.h - prefix OPA for src/config.h defines >> configure: ===== done with src/openpa configure ===== >> sourcing /Users/michael-steffen/Desktop/mpich-3.1.3/src/pm/hydra/mpichprereq >> checking whether the compiler defines __func__... yes >> checking whether the compiler defines __FUNC__... no >> checking whether the compiler sets __FUNCTION__... yes >> checking whether C compiler accepts option -O2... yes >> checking whether C compiler option -O2 works with an invalid prototype program... yes >> checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes >> checking for type of weak symbol alias support... no >> checking whether __attribute__ ((weak)) allowed... yes >> checking whether __attribute__ ((weak_import)) allowed... yes >> checking whether __attribute__((weak,alias(...))) allowed... no >> checking for shared library (esp. rpath) characteristics of CC... done (results in src/env/cc_shlib.conf) >> checking whether Fortran 77 compiler accepts option -O2... no >> checking how to get verbose linking output from ... configure: WARNING: compilation failed >> >> checking for Fortran 77 libraries of ... >> checking whether accepts the FLIBS found by autoconf... no >> checking for valid entries in FLIBS... >> checking whether gcc links with FLIBS found by autoconf... yes >> checking whether Fortran 77 and C objects are compatible... no >> checking for file... file >> configure: error: **** Incompatible Fortran and C Object File Types! **** >> F77 Object File Type produced by " " is : : cannot open `' (No such file or directory). >> C Object File Type produced by "gcc -O2" is : : Mach-O 64-bit object x86_64. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make >> make: *** No targets specified and no makefile found. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make |& tee m.txt >> -bash: syntax error near unexpected token `&' >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make | tee m.txt >> make: *** No targets specified and no makefile found. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make 2>&1 | tee m.txt >> make: *** No targets specified and no makefile found. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make clean >> make: *** No rule to make target `clean'. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 |& tee m.txt >> -bash: syntax error near unexpected token `&' >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 | tee m.txt >> make: *** No targets specified and no makefile found. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 tee m.txt >> make: *** No rule to make target `tee'. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 2>&1 | tee m.txt >> make: *** No targets specified and no makefile found. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 2>&1 tee m.txt >> make: *** No rule to make target `tee'. Stop. >> Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ >> >> >> Thanks, >> Mike >> -- >> Michael A. Steffen >> PhD. Candidate >> Department of Biological Sciences >> 800 S. Tucker Drive >> University of Tulsa >> Tulsa, OK 74104 >> Phone (708) 738-1491 >> _______________________________________________ >> 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 _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

1 0

Re: [mpich-discuss] trouble installing
by Lu, Huiwei 30 Oct '14

30 Oct '14

Thanks for reporting your install information. Looks like the configure didn’t detect your environment correctly. It should detect that you did not have fortran installed and should not check fortran bindings afterwards. Before we fix the configure, would you like to try the following first: if you do not need fortran, you can configure MPICH with ‘configure --disable-fortran’. If you need fortran, please install fortran compiler and try again. p.s. Michael: we are using discuss(a)mpich.org instead of mpich-discuss(a)mcs.anl.gov now. — Huiwei > On Oct 29, 2014, at 11:50 PM, Michael Steffen <michael-steffen(a)utulsa.edu> wrote: > > I am having trouble installing mpich on my macbook pro. > > This is what my terminal window looks like when I try to install it at get stuck at the make part. > > What am I doing wrong? > > Last login: Wed Oct 29 22:36:42 on ttys000 > Michaels-MacBook-Pro:~ michael-steffen$ cd /Users/michael-steffen/Desktop/mpich-3.1.3 > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ /Users/michael-steffen/Desktop/mpich-3.1.3/configure > Configuring MPICH version 3.1.3 > Running on system: Darwin Michaels-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 > checking for icc... no > checking for pgcc... no > checking for xlc... no > checking for xlC... no > checking for pathcc... no > checking for gcc... gcc > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking whether gcc understands -c and -o together... yes > checking how to run the C preprocessor... gcc -E > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... confdb/install-sh -c -d > checking for gawk... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > checking whether make sets $(MAKE)... yes > checking for style of include used by make... GNU > checking whether make supports nested variables... yes > checking dependency style of gcc... gcc3 > checking whether to enable maintainer-specific portions of Makefiles... yes > checking for ar... ar > checking the archiver (ar) interface... ar > checking build system type... x86_64-apple-darwin13.4.0 > checking host system type... x86_64-apple-darwin13.4.0 > checking how to print strings... printf > checking for a sed that does not truncate output... /usr/bin/sed > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for fgrep... /usr/bin/grep -F > checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld > checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm > checking the name lister (/usr/bin/nm) interface... BSD nm > checking whether ln -s works... yes > checking the maximum length of command line arguments... 196608 > checking whether the shell understands some XSI constructs... yes > checking whether the shell understands "+="... yes > checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop > checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r > checking for objdump... no > checking how to recognize dependent libraries... pass_all > checking for dlltool... no > checking how to associate runtime and link libraries... printf %s\n > checking for archiver @FILE support... no > checking for strip... strip > checking for ranlib... ranlib > checking command to parse /usr/bin/nm output from gcc object... ok > checking for sysroot... no > checking for mt... no > checking if : is a manifest tool... no > checking for dsymutil... dsymutil > checking for nmedit... nmedit > checking for lipo... lipo > checking for otool... otool > checking for otool64... no > checking for -single_module linker flag... yes > checking for -exported_symbols_list linker flag... yes > checking for -force_load linker flag... yes > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for dlfcn.h... yes > checking for objdir... .libs > checking if gcc supports -fno-rtti -fno-exceptions... yes > checking for gcc option to produce PIC... -fno-common -DPIC > checking if gcc PIC flag -fno-common -DPIC works... yes > checking if gcc static flag -static works... no > checking if gcc supports -c -o file.o... yes > checking if gcc supports -c -o file.o... (cached) yes > checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes > checking dynamic linker characteristics... darwin13.4.0 dyld > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > checking whether make supports nested variables... (cached) yes > checking for icpc... no > checking for pgCC... no > checking for xlC... no > checking for pathCC... no > checking for g++... g++ > checking whether we are using the GNU C++ compiler... yes > checking whether g++ accepts -g... yes > checking dependency style of g++... gcc3 > checking how to run the C++ preprocessor... g++ -E > checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld > checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no > checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes > checking for g++ option to produce PIC... -fno-common -DPIC > checking if g++ PIC flag -fno-common -DPIC works... yes > checking if g++ static flag -static works... no > checking if g++ supports -c -o file.o... yes > checking if g++ supports -c -o file.o... (cached) yes > checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes > checking dynamic linker characteristics... darwin13.4.0 dyld > checking how to hardcode library paths into programs... immediate > checking for ifort... no > checking for pgf90... no > checking for pathf90... no > checking for pathf95... no > checking for xlf90... no > checking for xlf95... no > checking for xlf2003... no > checking for gfortran... no > checking for f90... no > checking for epcf90... no > checking for f95... no > checking for fort... no > checking for lf95... no > checking for g95... no > checking for ifc... no > checking for efc... no > checking for gfc... no > checking whether we are using the GNU Fortran compiler... no > checking whether accepts -g... no > checking for ifort... no > checking for pgf77... no > checking for af77... no > checking for xlf... no > checking for frt... no > checking for cf77... no > checking for fort77... no > checking for fl32... no > checking for fort... no > checking for ifc... no > checking for efc... no > checking for ftn... no > checking for gfortran... no > checking for f77... no > checking for g77... no > checking whether we are using the GNU Fortran 77 compiler... no > checking whether accepts -g... no > checking hcoll/api/hcoll_api.h usability... no > checking hcoll/api/hcoll_api.h presence... no > checking for hcoll/api/hcoll_api.h... no > checking for hcoll_init in -lhcoll... no > configure: RUNNING PREREQ FOR ch3:nemesis > checking for getpagesize... yes > checking for getpagesize... (cached) yes > configure: ===== configuring src/mpl ===== > configure: running /bin/sh ./configure --disable-option-checking '--prefix=NONE' --cache-file=/dev/null --srcdir=. > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... confdb/install-sh -c -d > checking for gawk... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > checking whether make sets $(MAKE)... yes > checking whether make supports nested variables... yes > checking for style of include used by make... GNU > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking whether gcc understands -c and -o together... yes > checking dependency style of gcc... gcc3 > checking the archiver (ar) interface... ar > checking build system type... x86_64-apple-darwin13.4.0 > checking host system type... x86_64-apple-darwin13.4.0 > checking how to print strings... printf > checking for a sed that does not truncate output... /usr/bin/sed > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for fgrep... /usr/bin/grep -F > checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld > checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm > checking the name lister (/usr/bin/nm) interface... BSD nm > checking whether ln -s works... yes > checking the maximum length of command line arguments... 196608 > checking whether the shell understands some XSI constructs... yes > checking whether the shell understands "+="... yes > checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop > checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r > checking for objdump... no > checking how to recognize dependent libraries... pass_all > checking for dlltool... no > checking how to associate runtime and link libraries... printf %s\n > checking for archiver @FILE support... no > checking for strip... strip > checking for ranlib... ranlib > checking command to parse /usr/bin/nm output from gcc object... ok > checking for sysroot... no > checking for mt... no > checking if : is a manifest tool... no > checking for dsymutil... dsymutil > checking for nmedit... nmedit > checking for lipo... lipo > checking for otool... otool > checking for otool64... no > checking for -single_module linker flag... yes > checking for -exported_symbols_list linker flag... yes > checking for -force_load linker flag... yes > checking how to run the C preprocessor... gcc -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for dlfcn.h... yes > checking for objdir... .libs > checking if gcc supports -fno-rtti -fno-exceptions... yes > checking for gcc option to produce PIC... -fno-common -DPIC > checking if gcc PIC flag -fno-common -DPIC works... yes > checking if gcc static flag -static works... no > checking if gcc supports -c -o file.o... yes > checking if gcc supports -c -o file.o... (cached) yes > checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes > checking dynamic linker characteristics... darwin13.4.0 dyld > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > checking whether make supports nested variables... (cached) yes > checking for an ANSI C-conforming const... yes > checking for C/C++ restrict keyword... __restrict > checking for inline... inline > checking for variable argument list macro functionality... yes > checking for gcov... gcov > checking whether the compiler supports __typeof(variable)... yes > checking stdio.h usability... yes > checking stdio.h presence... yes > checking for stdio.h... yes > checking for stdlib.h... (cached) yes > checking for string.h... (cached) yes > checking stdarg.h usability... yes > checking stdarg.h presence... yes > checking for stdarg.h... yes > checking ctype.h usability... yes > checking ctype.h presence... yes > checking for ctype.h... yes > checking search.h usability... yes > checking search.h presence... yes > checking for search.h... yes > checking for sys/types.h... (cached) yes > checking sys/uio.h usability... yes > checking sys/uio.h presence... yes > checking for sys/uio.h... yes > checking for inttypes.h... (cached) yes > checking for stdint.h... (cached) yes > checking valgrind.h usability... no > checking valgrind.h presence... no > checking for valgrind.h... no > checking memcheck.h usability... no > checking memcheck.h presence... no > checking for memcheck.h... no > checking valgrind/valgrind.h usability... no > checking valgrind/valgrind.h presence... no > checking for valgrind/valgrind.h... no > checking valgrind/memcheck.h usability... no > checking valgrind/memcheck.h presence... no > checking for valgrind/memcheck.h... no > checking helgrind.h usability... no > checking helgrind.h presence... no > checking for helgrind.h... no > checking valgrind/helgrind.h usability... no > checking valgrind/helgrind.h presence... no > checking for valgrind/helgrind.h... no > checking drd.h usability... no > checking drd.h presence... no > checking for drd.h... no > checking valgrind/drd.h usability... no > checking valgrind/drd.h presence... no > checking for valgrind/drd.h... no > checking whether the valgrind headers are broken or too old... yes > checking for strdup... yes > checking whether strdup needs a declaration... no > checking for snprintf... yes > checking whether snprintf needs a declaration... no > checking for strncmp... yes > checking whether strncmp needs a declaration... no > checking for putenv... yes > checking whether putenv needs a declaration... no > checking whether __attribute__ allowed... yes > checking whether __attribute__((format)) allowed... yes > checking that generated files are newer than configure... done > configure: creating ./config.status > config.status: creating Makefile > config.status: creating localdefs > config.status: creating include/config.h > config.status: executing depfiles commands > config.status: executing libtool commands > config.status: executing include/mplconfig.h commands > config.status: creating include/mplconfig.h - prefix MPL for include/config.h defines > configure: ===== done with src/mpl configure ===== > configure: sourcing src/mpl/localdefs > configure: ===== configuring src/openpa ===== > configure: running /bin/sh ./configure --disable-option-checking '--prefix=NONE' --with-atomic-primitives=auto_allow_emulation --cache-file=/dev/null --srcdir=. > checking for a BSD-compatible install... /usr/bin/install -c > checking whether build environment is sane... yes > checking for a thread-safe mkdir -p... confdb/install-sh -c -d > checking for gawk... no > checking for mawk... no > checking for nawk... no > checking for awk... awk > checking whether make sets $(MAKE)... yes > checking whether make supports nested variables... yes > checking for style of include used by make... GNU > checking for gcc... gcc > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether gcc accepts -g... yes > checking for gcc option to accept ISO C89... none needed > checking whether gcc understands -c and -o together... yes > checking dependency style of gcc... gcc3 > checking the archiver (ar) interface... ar > checking build system type... x86_64-apple-darwin13.4.0 > checking host system type... x86_64-apple-darwin13.4.0 > checking how to print strings... printf > checking for a sed that does not truncate output... /usr/bin/sed > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for fgrep... /usr/bin/grep -F > checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld > checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm > checking the name lister (/usr/bin/nm) interface... BSD nm > checking whether ln -s works... yes > checking the maximum length of command line arguments... 196608 > checking whether the shell understands some XSI constructs... yes > checking whether the shell understands "+="... yes > checking how to convert x86_64-apple-darwin13.4.0 file names to x86_64-apple-darwin13.4.0 format... func_convert_file_noop > checking how to convert x86_64-apple-darwin13.4.0 file names to toolchain format... func_convert_file_noop > checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r > checking for objdump... no > checking how to recognize dependent libraries... pass_all > checking for dlltool... no > checking how to associate runtime and link libraries... printf %s\n > checking for archiver @FILE support... no > checking for strip... strip > checking for ranlib... ranlib > checking command to parse /usr/bin/nm output from gcc object... ok > checking for sysroot... no > checking for mt... no > checking if : is a manifest tool... no > checking for dsymutil... dsymutil > checking for nmedit... nmedit > checking for lipo... lipo > checking for otool... otool > checking for otool64... no > checking for -single_module linker flag... yes > checking for -exported_symbols_list linker flag... yes > checking for -force_load linker flag... yes > checking how to run the C preprocessor... gcc -E > checking for ANSI C header files... yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking for dlfcn.h... yes > checking for objdir... .libs > checking if gcc supports -fno-rtti -fno-exceptions... yes > checking for gcc option to produce PIC... -fno-common -DPIC > checking if gcc PIC flag -fno-common -DPIC works... yes > checking if gcc static flag -static works... no > checking if gcc supports -c -o file.o... yes > checking if gcc supports -c -o file.o... (cached) yes > checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes > checking dynamic linker characteristics... darwin13.4.0 dyld > checking how to hardcode library paths into programs... immediate > checking whether stripping libraries is possible... yes > checking if libtool supports shared libraries... yes > checking whether to build shared libraries... yes > checking whether to build static libraries... yes > checking whether make supports nested variables... (cached) yes > checking for gcc... (cached) gcc > checking whether we are using the GNU C compiler... (cached) yes > checking whether gcc accepts -g... (cached) yes > checking for gcc option to accept ISO C89... (cached) none needed > checking whether gcc understands -c and -o together... (cached) yes > checking dependency style of gcc... (cached) gcc3 > checking whether to enable assertions... yes > checking pthread.h usability... yes > checking pthread.h presence... yes > checking for pthread.h... yes > checking atomic.h usability... no > checking atomic.h presence... no > checking for atomic.h... no > checking intrin.h usability... no > checking intrin.h presence... no > checking for intrin.h... no > checking for inttypes.h... (cached) yes > checking for stdint.h... (cached) yes > checking stddef.h usability... yes > checking stddef.h presence... yes > checking for stddef.h... yes > checking for C/C++ restrict keyword... __restrict > checking for inline... inline > checking for an ANSI C-conforming const... yes > checking for pthread_create in -lpthread... yes > checking for pthread_yield... no > checking sched.h usability... yes > checking sched.h presence... yes > checking for sched.h... yes > checking for sched_yield... yes > checking if 100 threads can be run at once... yes > checking size of void *... 8 > checking size of int... 4 > checking whether __attribute__ allowed... yes > checking whether __attribute__((format)) allowed... yes > checking if compiler rejects bogus asm statements... yes > checking for support for gcc x86/x86_64 primitives... yes > checking for support for gcc x86 primitives for pre-Pentium 4... yes > checking for support for gcc ia64 primitives... no > checking for support for gcc PowerPC atomics... no > checking for support for gcc ARM atomics... no > checking for support for gcc SiCortex atomics... no > checking for support for gcc atomic intrinsics... yes > checking for support for Windows NT atomic intrinsics... no > checking for support for Sun atomic operations library... no > checking whether to enable strict fairness checks... no > checking that generated files are newer than configure... done > configure: creating ./config.status > config.status: creating Makefile > config.status: creating src/Makefile > config.status: creating test/Makefile > config.status: creating openpa.pc > config.status: creating src/config.h > config.status: executing depfiles commands > config.status: executing libtool commands > config.status: executing src/opa_config.h commands > config.status: creating src/opa_config.h - prefix OPA for src/config.h defines > configure: ===== done with src/openpa configure ===== > sourcing /Users/michael-steffen/Desktop/mpich-3.1.3/src/pm/hydra/mpichprereq > checking whether the compiler defines __func__... yes > checking whether the compiler defines __FUNC__... no > checking whether the compiler sets __FUNCTION__... yes > checking whether C compiler accepts option -O2... yes > checking whether C compiler option -O2 works with an invalid prototype program... yes > checking whether routines compiled with -O2 can be linked with ones compiled without -O2... yes > checking for type of weak symbol alias support... no > checking whether __attribute__ ((weak)) allowed... yes > checking whether __attribute__ ((weak_import)) allowed... yes > checking whether __attribute__((weak,alias(...))) allowed... no > checking for shared library (esp. rpath) characteristics of CC... done (results in src/env/cc_shlib.conf) > checking whether Fortran 77 compiler accepts option -O2... no > checking how to get verbose linking output from ... configure: WARNING: compilation failed > > checking for Fortran 77 libraries of ... > checking whether accepts the FLIBS found by autoconf... no > checking for valid entries in FLIBS... > checking whether gcc links with FLIBS found by autoconf... yes > checking whether Fortran 77 and C objects are compatible... no > checking for file... file > configure: error: **** Incompatible Fortran and C Object File Types! **** > F77 Object File Type produced by " " is : : cannot open `' (No such file or directory). > C Object File Type produced by "gcc -O2" is : : Mach-O 64-bit object x86_64. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make > make: *** No targets specified and no makefile found. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make |& tee m.txt > -bash: syntax error near unexpected token `&' > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make | tee m.txt > make: *** No targets specified and no makefile found. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make 2>&1 | tee m.txt > make: *** No targets specified and no makefile found. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make clean > make: *** No rule to make target `clean'. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 |& tee m.txt > -bash: syntax error near unexpected token `&' > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 | tee m.txt > make: *** No targets specified and no makefile found. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 tee m.txt > make: *** No rule to make target `tee'. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 2>&1 | tee m.txt > make: *** No targets specified and no makefile found. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ make VERBOSE=1 2>&1 tee m.txt > make: *** No rule to make target `tee'. Stop. > Michaels-MacBook-Pro:mpich-3.1.3 michael-steffen$ > > > Thanks, > Mike > -- > Michael A. Steffen > PhD. Candidate > Department of Biological Sciences > 800 S. Tucker Drive > University of Tulsa > Tulsa, OK 74104 > Phone (708) 738-1491 > _______________________________________________ > 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] discuss Digest, Vol 24, Issue 35
by Sean Delaney 30 Oct '14

30 Oct '14

Hi Rob, Thanks very much for your help. I’ve found some errors in my build process, which casts doubt over the how that assert statement was reached. I’m still getting erroneous behaviour from my code when I exceed 2GB read / write buffers per process, so there may be something more to this. I’ll continue working and get back to you if I can isolate a useful test case. Thanks again, Sean From: Latham, Robert J. [mailto:[email protected]] Sent: 29 October 2014 14:58 To: Sean Delaney; discuss Subject: Re: discuss Digest, Vol 24, Issue 35 I probably just need to ensure lustre picked up all changes from common code. Can you confirm your code works if you prefix the filename with "ufs:" ? ==rob -- sent from a phone From: Sean Delaney <Sean.Delaney(a)tullowoil.com<mailto:[email protected]>> Sent: Oct 29, 2014 9:54 AM To: discuss(a)mpich.org<mailto:[email protected]> Cc: Latham, Robert J. Subject: RE: discuss Digest, Vol 24, Issue 35 Hi Rob, Yes, this is mpich-3.1.3, as downloaded from the website in the last 2 days. I was alerted to the buf_idx[] overflow by a failing assert statement, which checks for overflow when assigning values to buf_idx[]. I'm running on lustre. I can't provide my current code as a test case. I may be able to prepare something later, but I need to focus on making my code work first. These variables have type 'int', whereas something like 'size_t' or 'ADIO_Offset' might be more appropriate to store buffer offsets, where constraints are not known. Sean ----------------------- this is in the latest 3.1.3 MPICH? I thought I bumped up the size of buf_idx and related fields, though my test cases are meager at best. Do you have a test case? Which file system? ==rob ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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