January 2016 - discuss - mailman3.cels.anl.gov

[PATCH] use libunwind only when both header and lib available
by Rob Latham 14 Jan '16

14 Jan '16

libunwind has runtime libraries and compile-time heaers. Some systems might provide libunwind without the corresponding -dev package. Be more careful about when to choose libunwind. --- src/mpl/src/bt/mpl_bt.c | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/mpl/src/bt/mpl_bt.c b/src/mpl/src/bt/mpl_bt.c index 5abd999d..3102a7a3 100644 --- a/src/mpl/src/bt/mpl_bt.c +++ b/src/mpl/src/bt/mpl_bt.c @@ -44,7 +44,11 @@ static inline void backtrace_libback(FILE *output) btstate = backtrace_create_state(NULL, 1, NULL, NULL); backtrace_print(btstate, 0, output); } -#elif defined MPL_HAVE_LIBUNWIND +/* we need not only the symbols but the header file too (for the cursor and + * context), so tighten up when we take the libunwind path. Thanks + * Siegmar.Gross(a)informatik.hs-fulda.de for the bug report about systems with + * libunwind libraries but no libunwind development headers */ +#if defined MPL_HAVE_LIBUNWIND && defined(MPL_HAVE_LIBUNWIND_H) static inline void backtrace_libunwind(FILE *output) { unw_cursor_t cursor; -- 2.5.0 --------------090807000004070201090607 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss --------------090807000004070201090607--

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Re: [mpich-discuss] valgrind warning in MPIR_Process_status
by Kenneth Raffenetti 14 Jan '16

14 Jan '16

This fix has been pushed into the main MPICH repo. Ken On 01/11/2016 06:44 AM, VandeVondele Joost wrote: > I can confirm that Daniel's patch also fixes the issue I was seeing. > > Thanks for the quick resolution. > > > ------------------------------------------------------------------------ > ------------------------------------------------------------------------ > *From:* Jeff Hammond [jeff.science(a)gmail.com] > *Sent:* Monday, January 11, 2016 6:51 AM > *To:* discuss(a)mpich.org > *Subject:* Re: [mpich-discuss] valgrind warning in MPIR_Process_status > > To be explicit, the other thread is > http://lists.mpich.org/pipermail/devel/2016-January/000677.html and it > is indeed the same issue. > > I pushed dibanez-helper_fns-valgrind to mpich-review just now. > https://trac.mpich.org/projects/mpich/ticket/2328 was created for > tracking purposes. > > Jeff > > On Sun, Jan 10, 2016 at 5:04 PM, Jeff Hammond <jeff.science(a)gmail.com > <mailto:[email protected]>> wrote: > > I think this is the same issue reported on the devel list yesterday. > If it is, Daniel Ibanez provided a patch that I've merged into my > (completely unofficial fork on github) and will push to the official > MPICH review repo tonight. > > If you want to try and/or verify Daniel'spatch, see > github/jeffhammond/mpich. The branch you want should be obvious from > the name (I can't remember what it is off hand). > > Best, > > Jeff > > > On Sunday, January 10, 2016, VandeVondele Joost > <joost.vandevondele(a)mat.ethz.ch > <mailto:[email protected]>> wrote: > > Hi, > > we upgraded from mpich 3.1.2 to 3.2 and our nightly builds under > valgrind show a new valgrind warning, which I suppose originates > from the mpi library, rather than our code (given the stack > trace below and the fact that they are absent with 3.1): > > There are two slightly distinct traces (alltoall and alltoallv): > > ==30165== Conditional jump or move depends on uninitialised value(s) > ==30165== at 0x6E00056: MPIR_Process_status (mpiimpl.h:4394) > ==30165== by 0x6E00056: MPIC_Waitall (helper_fns.c:774) > ==30165== by 0x6D5A853: MPIR_Alltoall_intra (alltoall.c:369) > ==30165== by 0x6D5B63C: MPIR_Alltoall (alltoall.c:564) > ==30165== by 0x6D5B6EF: MPIR_Alltoall_impl (alltoall.c:599) > ==30165== by 0x6D5BF07: PMPI_Alltoall (alltoall.c:722) > ==30165== by 0x6AFF0DC: PMPI_ALLTOALL (alltoallf.c:276) > ==30165== by 0x1D04699: __message_passing_MOD_mp_alltoall_i22 > > ==30201== Conditional jump or move depends on uninitialised value(s) > ==30201== at 0x6E00056: MPIR_Process_status (mpiimpl.h:4394) > ==30201== by 0x6E00056: MPIC_Waitall (helper_fns.c:774) > ==30201== by 0x6D5C4EA: MPIR_Alltoallv_intra (alltoallv.c:194) > ==30201== by 0x6D5CEC9: MPIR_Alltoallv (alltoallv.c:339) > ==30201== by 0x6D5CFAA: MPIR_Alltoallv_impl (alltoallv.c:376) > ==30201== by 0x6D5D8CA: PMPI_Alltoallv (alltoallv.c:527) > ==30201== by 0x6AFF13E: PMPI_ALLTOALLV (alltoallvf.c:276) > ==30201== by 0x1CCE180: > __message_passing_MOD_mp_alltoall_z22v (message_passing_z.f90:223) > > Is this issue already known/fixed ? > > I saw there was a somewhat related change (which is part of 3.2): > > https://trac.mpich.org/projects/mpich/changeset/be7c17b3177ccb0ede49761b44a… > > but maybe that change was not fully complete ? > > Best regards, > > Joost VandeVondele > > ------------------------------------------------------------------------ > Prof. Dr. Joost VandeVondele > Nanoscale Simulations > > ETH Zurich > HIT G 41.4 > Wolfgang-Pauli-Strasse 27 > 8093 Zurich, Switzerland > > Joost.VandeVondele(a)mat.ethz.ch > http://www.nanosim.mat.ethz.ch/ > Tel.: +41 (0)44 6338451 > ------------------------------------------------------------------------ > > > > -- > Jeff Hammond > jeff.science(a)gmail.com <mailto:[email protected]> > http://jeffhammond.github.io/ > > > > > -- > Jeff Hammond > jeff.science(a)gmail.com <mailto:[email protected]> > http://jeffhammond.github.io/ > > > _______________________________________________ > 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] Error buildingmpich-master-v3.2-88-gbbb40df74d46
by Rob Latham 14 Jan '16

14 Jan '16

On 01/14/2016 09:52 AM, Siegmar Gross wrote: > Hi, > > where can I find "version 77592165aa3"? I have only the following > archives after the release of mpich-3.2.tar.gz. > I misunderstood your setup. I thought you were working directly from our git repository, not from git snapshots. If you were working from a repository, you would do this: $ git checkout -b 3.2.1-77592165aa3 77592165aa3 > loki mpich-3.2.1 113 ls -C1 *.gz > mpich-master-v3.2-42-g67631a5c0e9e.tar.gz > mpich-master-v3.2-87-g7150bbc02ec8.tar.gz > mpich-master-v3.2-88-gbbb40df74d46.tar.gz g7150bbc02ec8 is too old to contain my changes. g67631a5c0e9e might be the one to try. > I've attached both config.log files from my gcc and cc version. config.log-gcc says the unw_backtrace symbol exists in libunwind, but there is no libunwind.h header file on your system. Looks like I need to be more careful in how I detect support for backtrace libraries. > I've searched for "libunwind tools" for our Linux version. It seems that > they are available for "Suse Linux Enterprise Server", but I didn't find > them for "Suse Linux Enterprise Desktop", which we use for most of our > machines. Shall I ask our Admin to install them? > what is supposed to happen is we look for several ways to generate a backtrace, then use the one we found. What's bothering me is that we think we found libunwind, but when we try to use libunwind's features we fail to compile. our configure should not report that libunwind is available if it is unusable. For example, our configure also found the backtrace_symbols and backtrace_create_state functions. These are often part of GCC, or maybe standalone in the libbacktrace package. On your system (as is common on many systems) there is no backtrace.h I will send you a patch to try out that will only use libunwind if it finds both the header file and the symbols. ==rob > > Best regards > > Siegmar > > > On 01/14/16 16:25, Rob Latham wrote: >> >> >> On 01/14/2016 07:21 AM, Siegmar Gross wrote: >>> Hi, >>> >>> today I tried to build mpich-master-v3.2-88-gbbb40df74d46 on my machine >>> (SUSE Linux Enterprise Server 12.0 x86_64) with gcc-5.2.0 and Sun C >>> 5.13. >>> I used the following command to build the system for gcc. >> >> This looks like the "portable backtrace" functionality I added >> recently. Maybe I need to work on the "portable" part >> of that. >> >> MPICH thinks your environment has the libunwind tools, and so it is >> trying to use libunwind to display the backtrace. >> >> Unfortunately there's one more complication: a reorganization of the >> MPL sources (commit 12c912ec6372). >> >> If you can provide me with two pieces of information that would be great: >> >> - what if you check out MPICH from a few weeks back? I want to rule >> out the source reorg, and if you check out version >> 77592165aa3, that will have just my changes and none of the reorg >> changes. >> >> - Can you send me your src/mpl/config.log ? (not the config.log from >> top-level mpich, but the config.log subconfigure >> from src/mpl) I would like to see what backtrace libraries configure >> found in your environment. Then I can reproduce >> it on my end. >> >> ==rob >> >>> >>> mkdir >>> mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc >>> cd >>> mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc >>> >>> ../mpich-master-v3.2-88-gbbb40df74d46/configure \ >>> --prefix=/usr/local/mpich-3.2.1_64_gcc \ >>> --libdir=/usr/local/mpich-3.2.1_64_gcc/lib64 \ >>> --includedir=/usr/local/mpich-3.2.1_64_gcc/include64 \ >>> CC="gcc" CXX="g++" F77="gfortran" FC="gfortran" \ >>> CFLAGS="-m64 -z noexecstack" CXXFLAGS="-m64" FFLAGS="-m64" >>> FCFLAGS="-m64" \ >>> LDFLAGS="-m64" \ >>> --enable-fortran=yes --enable-cxx --enable-romio \ >>> --enable-debuginfo --enable-smpcoll \ >>> --enable-threads=multiple --with-thread-package=posix \ >>> --enable-shared \ >>> |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc >>> >>> make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_gcc >>> >>> >>> "make" broke with the following error for "cc". >>> >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 111 cat >>> log.make.Linux.x86_64.64_cc >>> if test ! -h ./src/include/mpio.h ; then \ >>> rm -f ./src/include/mpio.h ; \ >>> ( cd ./src/include && \ >>> ln -s ../mpi/romio/include/mpio.h ) ; \ >>> fi >>> make all-recursive >>> make[1]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' >>> >>> >>> Making all in >>> /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl >>> >>> >>> make[2]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' >>> >>> >>> CC src/bt/mpl_bt.lo >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 50: undefined symbol: unw_cursor_t >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 50: syntax error before or at: cursor >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 51: undefined symbol: unw_context_t >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 52: undefined symbol: unw_word_t >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 57: warning: implicit function declaration: unw_getcontext >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 57: undefined symbol: uc >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 58: warning: implicit function declaration: unw_init_local >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 58: undefined symbol: cursor >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 59: warning: implicit function declaration: unw_step >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 60: warning: implicit function declaration: unw_get_reg >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 60: undefined symbol: UNW_REG_IP >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 60: undefined symbol: ip >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 61: warning: implicit function declaration: unw_get_proc_name >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 62: undefined symbol: offset >>> cc: acomp failed for >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c >>> Makefile:923: recipe for target 'src/bt/mpl_bt.lo' failed >>> make[2]: *** [src/bt/mpl_bt.lo] Error 1 >>> make[2]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' >>> >>> >>> Makefile:38434: recipe for target 'all-recursive' failed >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' >>> >>> >>> Makefile:10304: recipe for target 'all' failed >>> make: *** [all] Error 2 >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 112 >>> >>> >>> >>> "make" broke with the following error for "gcc". >>> >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 cat >>> log.make.Linux.x86_64.64_gcc >>> if test ! -h ./src/include/mpio.h ; then \ >>> rm -f ./src/include/mpio.h ; \ >>> ( cd ./src/include && \ >>> ln -s ../mpi/romio/include/mpio.h ) ; \ >>> fi >>> make all-recursive >>> make[1]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' >>> >>> >>> Making all in >>> /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl >>> >>> >>> make[2]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' >>> >>> >>> CC src/bt/mpl_bt.lo >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c: In >>> function ‘backtrace_libunwind’: >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:50:5: >>> error: >>> unknown type name ‘unw_cursor_t’ >>> unw_cursor_t cursor; >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:51:5: >>> error: >>> unknown type name ‘unw_context_t’ >>> unw_context_t uc; >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:52:5: >>> error: >>> unknown type name ‘unw_word_t’ >>> unw_word_t ip, offset; >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:57:5: >>> warning: >>> implicit declaration of function ‘unw_getcontext’ >>> [-Wimplicit-function-declaration] >>> unw_getcontext(&uc); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:58:5: >>> warning: >>> implicit declaration of function ‘unw_init_local’ >>> [-Wimplicit-function-declaration] >>> unw_init_local(&cursor, &uc); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:59:12: >>> >>> warning: implicit declaration of function ‘unw_step’ >>> [-Wimplicit-function-declaration] >>> while (unw_step(&cursor) > 0) { >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:9: >>> warning: >>> implicit declaration of function ‘unw_get_reg’ >>> [-Wimplicit-function-declaration] >>> unw_get_reg(&cursor, UNW_REG_IP, &ip); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: >>> >>> error: ‘UNW_REG_IP’ undeclared (first use in this function) >>> unw_get_reg(&cursor, UNW_REG_IP, &ip); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: >>> >>> note: each undeclared identifier is reported only once for each function >>> it appears in >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:61:9: >>> warning: >>> implicit declaration of function ‘unw_get_proc_name’ >>> [-Wimplicit-function-declaration] >>> unw_get_proc_name(&cursor, buffer, >>> ^ >>> Makefile:920: recipe for target 'src/bt/mpl_bt.lo' failed >>> make[2]: *** [src/bt/mpl_bt.lo] Error 1 >>> make[2]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' >>> >>> >>> Makefile:38434: recipe for target 'all-recursive' failed >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' >>> >>> >>> Makefile:10304: recipe for target 'all' failed >>> make: *** [all] Error 2 >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 >>> >>> >>> >>> I would be grateful if somebody can fix the problem. Thank you very >>> much for any help in advance. >>> >>> >>> Kind regards >>> >>> Siegmar >>> _______________________________________________ >>> 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 > _______________________________________________ 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] Error buildingmpich-master-v3.2-88-gbbb40df74d46
by Halim Amer 14 Jan '16

14 Jan '16

you can check out that version from our git repo: git clone http://git.mpich.org/mpich.git cd mpich git checkout 77592165aa3 --Halim www.mcs.anl.gov/~aamer On 1/14/16 9:52 AM, Siegmar Gross wrote: > Hi, > > where can I find "version 77592165aa3"? I have only the following > archives after the release of mpich-3.2.tar.gz. > > loki mpich-3.2.1 113 ls -C1 *.gz > mpich-master-v3.2-42-g67631a5c0e9e.tar.gz > mpich-master-v3.2-87-g7150bbc02ec8.tar.gz > mpich-master-v3.2-88-gbbb40df74d46.tar.gz > > I've attached both config.log files from my gcc and cc version. > > I've searched for "libunwind tools" for our Linux version. It seems that > they are available for "Suse Linux Enterprise Server", but I didn't find > them for "Suse Linux Enterprise Desktop", which we use for most of our > machines. Shall I ask our Admin to install them? > > > Best regards > > Siegmar > > > On 01/14/16 16:25, Rob Latham wrote: >> >> >> On 01/14/2016 07:21 AM, Siegmar Gross wrote: >>> Hi, >>> >>> today I tried to build mpich-master-v3.2-88-gbbb40df74d46 on my machine >>> (SUSE Linux Enterprise Server 12.0 x86_64) with gcc-5.2.0 and Sun C >>> 5.13. >>> I used the following command to build the system for gcc. >> >> This looks like the "portable backtrace" functionality I added >> recently. Maybe I need to work on the "portable" part >> of that. >> >> MPICH thinks your environment has the libunwind tools, and so it is >> trying to use libunwind to display the backtrace. >> >> Unfortunately there's one more complication: a reorganization of the >> MPL sources (commit 12c912ec6372). >> >> If you can provide me with two pieces of information that would be great: >> >> - what if you check out MPICH from a few weeks back? I want to rule >> out the source reorg, and if you check out version >> 77592165aa3, that will have just my changes and none of the reorg >> changes. >> >> - Can you send me your src/mpl/config.log ? (not the config.log from >> top-level mpich, but the config.log subconfigure >> from src/mpl) I would like to see what backtrace libraries configure >> found in your environment. Then I can reproduce >> it on my end. >> >> ==rob >> >>> >>> mkdir >>> mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc >>> cd >>> mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc >>> >>> ../mpich-master-v3.2-88-gbbb40df74d46/configure \ >>> --prefix=/usr/local/mpich-3.2.1_64_gcc \ >>> --libdir=/usr/local/mpich-3.2.1_64_gcc/lib64 \ >>> --includedir=/usr/local/mpich-3.2.1_64_gcc/include64 \ >>> CC="gcc" CXX="g++" F77="gfortran" FC="gfortran" \ >>> CFLAGS="-m64 -z noexecstack" CXXFLAGS="-m64" FFLAGS="-m64" >>> FCFLAGS="-m64" \ >>> LDFLAGS="-m64" \ >>> --enable-fortran=yes --enable-cxx --enable-romio \ >>> --enable-debuginfo --enable-smpcoll \ >>> --enable-threads=multiple --with-thread-package=posix \ >>> --enable-shared \ >>> |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc >>> >>> make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_gcc >>> >>> >>> "make" broke with the following error for "cc". >>> >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 111 cat >>> log.make.Linux.x86_64.64_cc >>> if test ! -h ./src/include/mpio.h ; then \ >>> rm -f ./src/include/mpio.h ; \ >>> ( cd ./src/include && \ >>> ln -s ../mpi/romio/include/mpio.h ) ; \ >>> fi >>> make all-recursive >>> make[1]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' >>> >>> >>> Making all in >>> /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl >>> >>> >>> make[2]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' >>> >>> >>> CC src/bt/mpl_bt.lo >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 50: undefined symbol: unw_cursor_t >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 50: syntax error before or at: cursor >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 51: undefined symbol: unw_context_t >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 52: undefined symbol: unw_word_t >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 57: warning: implicit function declaration: unw_getcontext >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 57: undefined symbol: uc >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 58: warning: implicit function declaration: unw_init_local >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 58: undefined symbol: cursor >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 59: warning: implicit function declaration: unw_step >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 60: warning: implicit function declaration: unw_get_reg >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 60: undefined symbol: UNW_REG_IP >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 60: undefined symbol: ip >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 61: warning: implicit function declaration: unw_get_proc_name >>> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >>> line 62: undefined symbol: offset >>> cc: acomp failed for >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c >>> Makefile:923: recipe for target 'src/bt/mpl_bt.lo' failed >>> make[2]: *** [src/bt/mpl_bt.lo] Error 1 >>> make[2]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' >>> >>> >>> Makefile:38434: recipe for target 'all-recursive' failed >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' >>> >>> >>> Makefile:10304: recipe for target 'all' failed >>> make: *** [all] Error 2 >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 112 >>> >>> >>> >>> "make" broke with the following error for "gcc". >>> >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 cat >>> log.make.Linux.x86_64.64_gcc >>> if test ! -h ./src/include/mpio.h ; then \ >>> rm -f ./src/include/mpio.h ; \ >>> ( cd ./src/include && \ >>> ln -s ../mpi/romio/include/mpio.h ) ; \ >>> fi >>> make all-recursive >>> make[1]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' >>> >>> >>> Making all in >>> /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl >>> >>> >>> make[2]: Entering directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' >>> >>> >>> CC src/bt/mpl_bt.lo >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c: In >>> function ‘backtrace_libunwind’: >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:50:5: >>> error: >>> unknown type name ‘unw_cursor_t’ >>> unw_cursor_t cursor; >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:51:5: >>> error: >>> unknown type name ‘unw_context_t’ >>> unw_context_t uc; >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:52:5: >>> error: >>> unknown type name ‘unw_word_t’ >>> unw_word_t ip, offset; >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:57:5: >>> warning: >>> implicit declaration of function ‘unw_getcontext’ >>> [-Wimplicit-function-declaration] >>> unw_getcontext(&uc); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:58:5: >>> warning: >>> implicit declaration of function ‘unw_init_local’ >>> [-Wimplicit-function-declaration] >>> unw_init_local(&cursor, &uc); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:59:12: >>> >>> warning: implicit declaration of function ‘unw_step’ >>> [-Wimplicit-function-declaration] >>> while (unw_step(&cursor) > 0) { >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:9: >>> warning: >>> implicit declaration of function ‘unw_get_reg’ >>> [-Wimplicit-function-declaration] >>> unw_get_reg(&cursor, UNW_REG_IP, &ip); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: >>> >>> error: ‘UNW_REG_IP’ undeclared (first use in this function) >>> unw_get_reg(&cursor, UNW_REG_IP, &ip); >>> ^ >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: >>> >>> note: each undeclared identifier is reported only once for each function >>> it appears in >>> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:61:9: >>> warning: >>> implicit declaration of function ‘unw_get_proc_name’ >>> [-Wimplicit-function-declaration] >>> unw_get_proc_name(&cursor, buffer, >>> ^ >>> Makefile:920: recipe for target 'src/bt/mpl_bt.lo' failed >>> make[2]: *** [src/bt/mpl_bt.lo] Error 1 >>> make[2]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' >>> >>> >>> Makefile:38434: recipe for target 'all-recursive' failed >>> make[1]: *** [all-recursive] Error 1 >>> make[1]: Leaving directory >>> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' >>> >>> >>> Makefile:10304: recipe for target 'all' failed >>> make: *** [all] Error 2 >>> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 >>> >>> >>> >>> I would be grateful if somebody can fix the problem. Thank you very >>> much for any help in advance. >>> >>> >>> Kind regards >>> >>> Siegmar >>> _______________________________________________ >>> 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 > _______________________________________________ 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] Error buildingmpich-master-v3.2-88-gbbb40df74d46
by Siegmar Gross 14 Jan '16

14 Jan '16

Hi, where can I find "version 77592165aa3"? I have only the following archives after the release of mpich-3.2.tar.gz. loki mpich-3.2.1 113 ls -C1 *.gz mpich-master-v3.2-42-g67631a5c0e9e.tar.gz mpich-master-v3.2-87-g7150bbc02ec8.tar.gz mpich-master-v3.2-88-gbbb40df74d46.tar.gz I've attached both config.log files from my gcc and cc version. I've searched for "libunwind tools" for our Linux version. It seems that they are available for "Suse Linux Enterprise Server", but I didn't find them for "Suse Linux Enterprise Desktop", which we use for most of our machines. Shall I ask our Admin to install them? Best regards Siegmar On 01/14/16 16:25, Rob Latham wrote: > > > On 01/14/2016 07:21 AM, Siegmar Gross wrote: >> Hi, >> >> today I tried to build mpich-master-v3.2-88-gbbb40df74d46 on my machine >> (SUSE Linux Enterprise Server 12.0 x86_64) with gcc-5.2.0 and Sun C 5.13. >> I used the following command to build the system for gcc. > > This looks like the "portable backtrace" functionality I added recently. Maybe I need to work on the "portable" part > of that. > > MPICH thinks your environment has the libunwind tools, and so it is trying to use libunwind to display the backtrace. > > Unfortunately there's one more complication: a reorganization of the MPL sources (commit 12c912ec6372). > > If you can provide me with two pieces of information that would be great: > > - what if you check out MPICH from a few weeks back? I want to rule out the source reorg, and if you check out version > 77592165aa3, that will have just my changes and none of the reorg changes. > > - Can you send me your src/mpl/config.log ? (not the config.log from top-level mpich, but the config.log subconfigure > from src/mpl) I would like to see what backtrace libraries configure found in your environment. Then I can reproduce > it on my end. > > ==rob > >> >> mkdir >> mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc >> cd mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc >> >> ../mpich-master-v3.2-88-gbbb40df74d46/configure \ >> --prefix=/usr/local/mpich-3.2.1_64_gcc \ >> --libdir=/usr/local/mpich-3.2.1_64_gcc/lib64 \ >> --includedir=/usr/local/mpich-3.2.1_64_gcc/include64 \ >> CC="gcc" CXX="g++" F77="gfortran" FC="gfortran" \ >> CFLAGS="-m64 -z noexecstack" CXXFLAGS="-m64" FFLAGS="-m64" >> FCFLAGS="-m64" \ >> LDFLAGS="-m64" \ >> --enable-fortran=yes --enable-cxx --enable-romio \ >> --enable-debuginfo --enable-smpcoll \ >> --enable-threads=multiple --with-thread-package=posix \ >> --enable-shared \ >> |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc >> >> make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_gcc >> >> >> "make" broke with the following error for "cc". >> >> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 111 cat >> log.make.Linux.x86_64.64_cc >> if test ! -h ./src/include/mpio.h ; then \ >> rm -f ./src/include/mpio.h ; \ >> ( cd ./src/include && \ >> ln -s ../mpi/romio/include/mpio.h ) ; \ >> fi >> make all-recursive >> make[1]: Entering directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' >> >> Making all in >> /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl >> >> make[2]: Entering directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' >> >> CC src/bt/mpl_bt.lo >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 50: undefined symbol: unw_cursor_t >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 50: syntax error before or at: cursor >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 51: undefined symbol: unw_context_t >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 52: undefined symbol: unw_word_t >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 57: warning: implicit function declaration: unw_getcontext >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 57: undefined symbol: uc >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 58: warning: implicit function declaration: unw_init_local >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 58: undefined symbol: cursor >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 59: warning: implicit function declaration: unw_step >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 60: warning: implicit function declaration: unw_get_reg >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 60: undefined symbol: UNW_REG_IP >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 60: undefined symbol: ip >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 61: warning: implicit function declaration: unw_get_proc_name >> "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", >> line 62: undefined symbol: offset >> cc: acomp failed for >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c >> Makefile:923: recipe for target 'src/bt/mpl_bt.lo' failed >> make[2]: *** [src/bt/mpl_bt.lo] Error 1 >> make[2]: Leaving directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' >> >> Makefile:38434: recipe for target 'all-recursive' failed >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' >> >> Makefile:10304: recipe for target 'all' failed >> make: *** [all] Error 2 >> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 112 >> >> >> >> "make" broke with the following error for "gcc". >> >> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 cat >> log.make.Linux.x86_64.64_gcc >> if test ! -h ./src/include/mpio.h ; then \ >> rm -f ./src/include/mpio.h ; \ >> ( cd ./src/include && \ >> ln -s ../mpi/romio/include/mpio.h ) ; \ >> fi >> make all-recursive >> make[1]: Entering directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' >> >> Making all in >> /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl >> >> make[2]: Entering directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' >> >> CC src/bt/mpl_bt.lo >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c: In >> function ‘backtrace_libunwind’: >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:50:5: error: >> unknown type name ‘unw_cursor_t’ >> unw_cursor_t cursor; >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:51:5: error: >> unknown type name ‘unw_context_t’ >> unw_context_t uc; >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:52:5: error: >> unknown type name ‘unw_word_t’ >> unw_word_t ip, offset; >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:57:5: warning: >> implicit declaration of function ‘unw_getcontext’ >> [-Wimplicit-function-declaration] >> unw_getcontext(&uc); >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:58:5: warning: >> implicit declaration of function ‘unw_init_local’ >> [-Wimplicit-function-declaration] >> unw_init_local(&cursor, &uc); >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:59:12: >> warning: implicit declaration of function ‘unw_step’ >> [-Wimplicit-function-declaration] >> while (unw_step(&cursor) > 0) { >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:9: warning: >> implicit declaration of function ‘unw_get_reg’ >> [-Wimplicit-function-declaration] >> unw_get_reg(&cursor, UNW_REG_IP, &ip); >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: >> error: ‘UNW_REG_IP’ undeclared (first use in this function) >> unw_get_reg(&cursor, UNW_REG_IP, &ip); >> ^ >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: >> note: each undeclared identifier is reported only once for each function >> it appears in >> ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:61:9: warning: >> implicit declaration of function ‘unw_get_proc_name’ >> [-Wimplicit-function-declaration] >> unw_get_proc_name(&cursor, buffer, >> ^ >> Makefile:920: recipe for target 'src/bt/mpl_bt.lo' failed >> make[2]: *** [src/bt/mpl_bt.lo] Error 1 >> make[2]: Leaving directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' >> >> Makefile:38434: recipe for target 'all-recursive' failed >> make[1]: *** [all-recursive] Error 1 >> make[1]: Leaving directory >> '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' >> >> Makefile:10304: recipe for target 'all' failed >> make: *** [all] Error 2 >> loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 >> >> >> >> I would be grateful if somebody can fix the problem. Thank you very >> much for any help in advance. >> >> >> Kind regards >> >> Siegmar >> _______________________________________________ >> 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] Error building mpich-master-v3.2-88-gbbb40df74d46
by Rob Latham 14 Jan '16

14 Jan '16

On 01/14/2016 07:21 AM, Siegmar Gross wrote: > Hi, > > today I tried to build mpich-master-v3.2-88-gbbb40df74d46 on my machine > (SUSE Linux Enterprise Server 12.0 x86_64) with gcc-5.2.0 and Sun C 5.13. > I used the following command to build the system for gcc. This looks like the "portable backtrace" functionality I added recently. Maybe I need to work on the "portable" part of that. MPICH thinks your environment has the libunwind tools, and so it is trying to use libunwind to display the backtrace. Unfortunately there's one more complication: a reorganization of the MPL sources (commit 12c912ec6372). If you can provide me with two pieces of information that would be great: - what if you check out MPICH from a few weeks back? I want to rule out the source reorg, and if you check out version 77592165aa3, that will have just my changes and none of the reorg changes. - Can you send me your src/mpl/config.log ? (not the config.log from top-level mpich, but the config.log subconfigure from src/mpl) I would like to see what backtrace libraries configure found in your environment. Then I can reproduce it on my end. ==rob > > mkdir > mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc > cd mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc > > ../mpich-master-v3.2-88-gbbb40df74d46/configure \ > --prefix=/usr/local/mpich-3.2.1_64_gcc \ > --libdir=/usr/local/mpich-3.2.1_64_gcc/lib64 \ > --includedir=/usr/local/mpich-3.2.1_64_gcc/include64 \ > CC="gcc" CXX="g++" F77="gfortran" FC="gfortran" \ > CFLAGS="-m64 -z noexecstack" CXXFLAGS="-m64" FFLAGS="-m64" > FCFLAGS="-m64" \ > LDFLAGS="-m64" \ > --enable-fortran=yes --enable-cxx --enable-romio \ > --enable-debuginfo --enable-smpcoll \ > --enable-threads=multiple --with-thread-package=posix \ > --enable-shared \ > |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc > > make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_gcc > > > "make" broke with the following error for "cc". > > loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 111 cat > log.make.Linux.x86_64.64_cc > if test ! -h ./src/include/mpio.h ; then \ > rm -f ./src/include/mpio.h ; \ > ( cd ./src/include && \ > ln -s ../mpi/romio/include/mpio.h ) ; \ > fi > make all-recursive > make[1]: Entering directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' > > Making all in > /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl > > make[2]: Entering directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' > > CC src/bt/mpl_bt.lo > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 50: undefined symbol: unw_cursor_t > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 50: syntax error before or at: cursor > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 51: undefined symbol: unw_context_t > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 52: undefined symbol: unw_word_t > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 57: warning: implicit function declaration: unw_getcontext > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 57: undefined symbol: uc > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 58: warning: implicit function declaration: unw_init_local > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 58: undefined symbol: cursor > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 59: warning: implicit function declaration: unw_step > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 60: warning: implicit function declaration: unw_get_reg > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 60: undefined symbol: UNW_REG_IP > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 60: undefined symbol: ip > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 61: warning: implicit function declaration: unw_get_proc_name > "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", > line 62: undefined symbol: offset > cc: acomp failed for > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c > Makefile:923: recipe for target 'src/bt/mpl_bt.lo' failed > make[2]: *** [src/bt/mpl_bt.lo] Error 1 > make[2]: Leaving directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' > > Makefile:38434: recipe for target 'all-recursive' failed > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' > > Makefile:10304: recipe for target 'all' failed > make: *** [all] Error 2 > loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 112 > > > > "make" broke with the following error for "gcc". > > loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 cat > log.make.Linux.x86_64.64_gcc > if test ! -h ./src/include/mpio.h ; then \ > rm -f ./src/include/mpio.h ; \ > ( cd ./src/include && \ > ln -s ../mpi/romio/include/mpio.h ) ; \ > fi > make all-recursive > make[1]: Entering directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' > > Making all in > /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl > > make[2]: Entering directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' > > CC src/bt/mpl_bt.lo > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c: In > function ‘backtrace_libunwind’: > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:50:5: error: > unknown type name ‘unw_cursor_t’ > unw_cursor_t cursor; > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:51:5: error: > unknown type name ‘unw_context_t’ > unw_context_t uc; > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:52:5: error: > unknown type name ‘unw_word_t’ > unw_word_t ip, offset; > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:57:5: warning: > implicit declaration of function ‘unw_getcontext’ > [-Wimplicit-function-declaration] > unw_getcontext(&uc); > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:58:5: warning: > implicit declaration of function ‘unw_init_local’ > [-Wimplicit-function-declaration] > unw_init_local(&cursor, &uc); > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:59:12: > warning: implicit declaration of function ‘unw_step’ > [-Wimplicit-function-declaration] > while (unw_step(&cursor) > 0) { > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:9: warning: > implicit declaration of function ‘unw_get_reg’ > [-Wimplicit-function-declaration] > unw_get_reg(&cursor, UNW_REG_IP, &ip); > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: > error: ‘UNW_REG_IP’ undeclared (first use in this function) > unw_get_reg(&cursor, UNW_REG_IP, &ip); > ^ > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: > note: each undeclared identifier is reported only once for each function > it appears in > ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:61:9: warning: > implicit declaration of function ‘unw_get_proc_name’ > [-Wimplicit-function-declaration] > unw_get_proc_name(&cursor, buffer, > ^ > Makefile:920: recipe for target 'src/bt/mpl_bt.lo' failed > make[2]: *** [src/bt/mpl_bt.lo] Error 1 > make[2]: Leaving directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' > > Makefile:38434: recipe for target 'all-recursive' failed > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory > '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' > > Makefile:10304: recipe for target 'all' failed > make: *** [all] Error 2 > loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 > > > > I would be grateful if somebody can fix the problem. Thank you very > much for any help in advance. > > > Kind regards > > Siegmar > _______________________________________________ > 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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Error building mpich-master-v3.2-88-gbbb40df74d46
by Siegmar Gross 14 Jan '16

14 Jan '16

Hi, today I tried to build mpich-master-v3.2-88-gbbb40df74d46 on my machine (SUSE Linux Enterprise Server 12.0 x86_64) with gcc-5.2.0 and Sun C 5.13. I used the following command to build the system for gcc. mkdir mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc cd mpich-master-v3.2-88-gbbb40df74d46-${SYSTEM_ENV}.${MACHINE_ENV}.64_gcc ../mpich-master-v3.2-88-gbbb40df74d46/configure \ --prefix=/usr/local/mpich-3.2.1_64_gcc \ --libdir=/usr/local/mpich-3.2.1_64_gcc/lib64 \ --includedir=/usr/local/mpich-3.2.1_64_gcc/include64 \ CC="gcc" CXX="g++" F77="gfortran" FC="gfortran" \ CFLAGS="-m64 -z noexecstack" CXXFLAGS="-m64" FFLAGS="-m64" FCFLAGS="-m64" \ LDFLAGS="-m64" \ --enable-fortran=yes --enable-cxx --enable-romio \ --enable-debuginfo --enable-smpcoll \ --enable-threads=multiple --with-thread-package=posix \ --enable-shared \ |& tee log.configure.$SYSTEM_ENV.$MACHINE_ENV.64_gcc make |& tee log.make.$SYSTEM_ENV.$MACHINE_ENV.64_gcc "make" broke with the following error for "cc". loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 111 cat log.make.Linux.x86_64.64_cc if test ! -h ./src/include/mpio.h ; then \ rm -f ./src/include/mpio.h ; \ ( cd ./src/include && \ ln -s ../mpi/romio/include/mpio.h ) ; \ fi make all-recursive make[1]: Entering directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' Making all in /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl make[2]: Entering directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' CC src/bt/mpl_bt.lo "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 50: undefined symbol: unw_cursor_t "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 50: syntax error before or at: cursor "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 51: undefined symbol: unw_context_t "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 52: undefined symbol: unw_word_t "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 57: warning: implicit function declaration: unw_getcontext "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 57: undefined symbol: uc "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 58: warning: implicit function declaration: unw_init_local "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 58: undefined symbol: cursor "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 59: warning: implicit function declaration: unw_step "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 60: warning: implicit function declaration: unw_get_reg "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 60: undefined symbol: UNW_REG_IP "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 60: undefined symbol: ip "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 61: warning: implicit function declaration: unw_get_proc_name "../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c", line 62: undefined symbol: offset cc: acomp failed for ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c Makefile:923: recipe for target 'src/bt/mpl_bt.lo' failed make[2]: *** [src/bt/mpl_bt.lo] Error 1 make[2]: Leaving directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc/src/mpl' Makefile:38434: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc' Makefile:10304: recipe for target 'all' failed make: *** [all] Error 2 loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_cc 112 "make" broke with the following error for "gcc". loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 cat log.make.Linux.x86_64.64_gcc if test ! -h ./src/include/mpio.h ; then \ rm -f ./src/include/mpio.h ; \ ( cd ./src/include && \ ln -s ../mpi/romio/include/mpio.h ) ; \ fi make all-recursive make[1]: Entering directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' Making all in /export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl make[2]: Entering directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' CC src/bt/mpl_bt.lo ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c: In function ‘backtrace_libunwind’: ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:50:5: error: unknown type name ‘unw_cursor_t’ unw_cursor_t cursor; ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:51:5: error: unknown type name ‘unw_context_t’ unw_context_t uc; ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:52:5: error: unknown type name ‘unw_word_t’ unw_word_t ip, offset; ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:57:5: warning: implicit declaration of function ‘unw_getcontext’ [-Wimplicit-function-declaration] unw_getcontext(&uc); ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:58:5: warning: implicit declaration of function ‘unw_init_local’ [-Wimplicit-function-declaration] unw_init_local(&cursor, &uc); ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:59:12: warning: implicit declaration of function ‘unw_step’ [-Wimplicit-function-declaration] while (unw_step(&cursor) > 0) { ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:9: warning: implicit declaration of function ‘unw_get_reg’ [-Wimplicit-function-declaration] unw_get_reg(&cursor, UNW_REG_IP, &ip); ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: error: ‘UNW_REG_IP’ undeclared (first use in this function) unw_get_reg(&cursor, UNW_REG_IP, &ip); ^ ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:60:30: note: each undeclared identifier is reported only once for each function it appears in ../../../mpich-master-v3.2-88-gbbb40df74d46/src/mpl/src/bt/mpl_bt.c:61:9: warning: implicit declaration of function ‘unw_get_proc_name’ [-Wimplicit-function-declaration] unw_get_proc_name(&cursor, buffer, ^ Makefile:920: recipe for target 'src/bt/mpl_bt.lo' failed make[2]: *** [src/bt/mpl_bt.lo] Error 1 make[2]: Leaving directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc/src/mpl' Makefile:38434: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/export2/src/mpich-3.2.1/mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc' Makefile:10304: recipe for target 'all' failed make: *** [all] Error 2 loki mpich-master-v3.2-88-gbbb40df74d46-Linux.x86_64.64_gcc 114 I would be grateful if somebody can fix the problem. Thank you very much for any help in advance. Kind regards Siegmar _______________________________________________ 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] Running mpich3 on multiple machines
by Balaji, Pavan 13 Jan '16

13 Jan '16

Looks like your ssh is not fully setup. > On Jan 13, 2016, at 1:04 PM, Doha Ehab <dohaehab(a)gmail.com> wrote: > > Host 'sams' is not in the trusted hosts file. > (fingerprint md5 1c:c2:ee:33:9c:80:ae:9d:2c:b7:9f:7e:64:c2:87:e2) > Do you want to continue connecting? (y/n) y > ^C[mpiexec@samplus] Sending Ctrl-C to processes as requested > _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Running mpich3 on multiple machines
by Doha Ehab 13 Jan '16

13 Jan '16

Hello, I have crossed compiled mpich3.2 and it runs perfectly on a single machine but when I try it on 2 machines it hangs. (the ssh is working without mpich).here is the command I'm using . any suggestions mpiexec.hydra -verbose --host sams,samplus -launcher ssh -n 2 -l hostname host: sams host: samplus ================================================================================================== mpiexec options: ---------------- Base path: /system/xbin/ Launcher: ssh Debug level: 1 Enable X: -1 Global environment: ------------------- ANDROID_ROOT=/system LD_LIBRARY_PATH=/vendor/lib:/system/lib PATH=/sbin:/vendor/bin:/system/sbin:/system/bin:/system/xbin LOOP_MOUNTPOINT=/mnt/obb ASEC_MOUNTPOINT=/mnt/asec EXTERNAL_STORAGE2=/mnt/sdcard/external_sd BOOTCLASSPATH=/system/framework/core.jar:/system/framework/bouncycastle.jar:/system/framework/ext.jar:/system/framework/framework.jar:/system/framework/android.policy.jar:/system/framework/services.jar:/system/framework/core-junit.jar ANDROID_BOOTLOGO=1 ANDROID_ASSETS=/system/app EXTERNAL_STORAGE=/mnt/sdcard ANDROID_DATA=/data USBHOST_STORAGE=/mnt/sdcard/usbStorage ANDROID_PROPERTY_WORKSPACE=9,65536 Hydra internal environment: --------------------------- GFORTRAN_UNBUFFERED_PRECONNECTED=y Proxy information: ********************* [1] proxy: sams (1 cores) Exec list: hostname (1 processes); [2] proxy: samplus (1 cores) Exec list: hostname (1 processes); ================================================================================================== [mpiexec@samplus] Timeout set to -1 (-1 means infinite) [mpiexec@samplus] Got a control port string of samplus:36339 Proxy launch args: /system/xbin/hydra_pmi_proxy --control-port samplus:36339 --debug --rmk user --launcher ssh --demux poll --pgid 0 --retries 10 --usize -2 --proxy-id Arguments being passed to proxy 0: --version 3.2 --iface-ip-env-name MPIR_CVAR_CH3_INTERFACE_HOSTNAME --hostname sams --global-core-map 0,1,2 --pmi-id-map 0,0 --global-process-count 2 --auto-cleanup 1 --pmi-kvsname kvs_3105_0 --pmi-process-mapping (vector,(0,2,1)) --ckpoint-num -1 --global-inherited-env 13 'ANDROID_ROOT=/system' 'LD_LIBRARY_PATH=/vendor/lib:/system/lib' 'PATH=/sbin:/vendor/bin:/system/sbin:/system/bin:/system/xbin' 'LOOP_MOUNTPOINT=/mnt/obb' 'ASEC_MOUNTPOINT=/mnt/asec' 'EXTERNAL_STORAGE2=/mnt/sdcard/external_sd' 'BOOTCLASSPATH=/system/framework/core.jar:/system/framework/bouncycastle.jar:/system/framework/ext.jar:/system/framework/framework.jar:/system/framework/android.policy.jar:/system/framework/services.jar:/system/framework/core-junit.jar' 'ANDROID_BOOTLOGO=1' 'ANDROID_ASSETS=/system/app' 'EXTERNAL_STORAGE=/mnt/sdcard' 'ANDROID_DATA=/data' 'USBHOST_STORAGE=/mnt/sdcard/usbStorage' 'ANDROID_PROPERTY_WORKSPACE=9,65536' --global-user-env 0 --global-system-env 1 'GFORTRAN_UNBUFFERED_PRECONNECTED=y' --proxy-core-count 1 --exec --exec-appnum 0 --exec-proc-count 1 --exec-local-env 0 --exec-wdir / --exec-args 1 hostname Arguments being passed to proxy 1: --version 3.2 --iface-ip-env-name MPIR_CVAR_CH3_INTERFACE_HOSTNAME --hostname samplus --global-core-map 0,1,2 --pmi-id-map 0,1 --global-process-count 2 --auto-cleanup 1 --pmi-kvsname kvs_3105_0 --pmi-process-mapping (vector,(0,2,1)) --ckpoint-num -1 --global-inherited-env 13 'ANDROID_ROOT=/system' 'LD_LIBRARY_PATH=/vendor/lib:/system/lib' 'PATH=/sbin:/vendor/bin:/system/sbin:/system/bin:/system/xbin' 'LOOP_MOUNTPOINT=/mnt/obb' 'ASEC_MOUNTPOINT=/mnt/asec' 'EXTERNAL_STORAGE2=/mnt/sdcard/external_sd' 'BOOTCLASSPATH=/system/framework/core.jar:/system/framework/bouncycastle.jar:/system/framework/ext.jar:/system/framework/framework.jar:/system/framework/android.policy.jar:/system/framework/services.jar:/system/framework/core-junit.jar' 'ANDROID_BOOTLOGO=1' 'ANDROID_ASSETS=/system/app' 'EXTERNAL_STORAGE=/mnt/sdcard' 'ANDROID_DATA=/data' 'USBHOST_STORAGE=/mnt/sdcard/usbStorage' 'ANDROID_PROPERTY_WORKSPACE=9,65536' --global-user-env 0 --global-system-env 1 'GFORTRAN_UNBUFFERED_PRECONNECTED=y' --proxy-core-count 1 --exec --exec-appnum 0 --exec-proc-count 1 --exec-local-env 0 --exec-wdir / --exec-args 1 hostname [mpiexec@samplus] Launch arguments: /system/xbin/ssh -x sams "/system/xbin/hydra_pmi_proxy" --control-port samplus:36339 --debug --rmk user --launcher ssh --demux poll --pgid 0 --retries 10 --usize -2 --proxy-id 0 [mpiexec@samplus] Launch arguments: /system/xbin/hydra_pmi_proxy --control-port samplus:36339 --debug --rmk user --launcher ssh --demux poll --pgid 0 --retries 10 --usize -2 --proxy-id 1 WARNING: Ignoring unknown argument '-x' [1] samplus Host 'sams' is not in the trusted hosts file. (fingerprint md5 1c:c2:ee:33:9c:80:ae:9d:2c:b7:9f:7e:64:c2:87:e2) Do you want to continue connecting? (y/n) y ^C[mpiexec@samplus] Sending Ctrl-C to processes as requested [mpiexec@samplus] Press Ctrl-C again to force abort [mpiexec@samplus] HYDU_sock_write (utils/sock/sock.c:286): write error (Bad file descriptor) [mpiexec@samplus] HYD_pmcd_pmiserv_send_signal (pm/pmiserv/pmiserv_cb.c:169): unable to write data to proxy [mpiexec@samplus] ui_cmd_cb (pm/pmiserv/pmiserv_pmci.c:79): unable to send signal downstream [mpiexec@samplus] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status [mpiexec@samplus] HYD_pmci_wait_for_completion (pm/pmiserv/pmiserv_pmci.c:198): error waiting for event [mpiexec@samplus] main (ui/mpich/mpiexec.c:344): process manager error waiting for completion _______________________________________________ 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] single node mpiio
by Rob Latham 12 Jan '16

12 Jan '16

On 01/12/2016 02:01 PM, Jaln wrote: > Thanks Rob, > What is the reason of the whole file lock? is it due the bug in lustre > 2.5? which has been fixed in 2.6 and 2.7. > Or is it just due to such I/O pattern? > If without file-locking, is the "single link" to the 10 osts actually > blocking the I/O from being true parallel I/O? As Wei-keng clarified, the whole-file lock and subsequent revocation only matters when two or more nodes (not merely MPI processes, if they are on the same node) are involved. I don't know anything about a bug in lustre-2.5 I think this was a design choice -- while Lustre allows parallel access the design assumption is that most accesses are serial. Something like O_DIRECT can bypass the locking. When creating a file with a non-default stripe (and by default Lustre stripes are typically 1 or 4, not "all available OSTs), ROMIO's lustre driver will set the O_LOV_DELAY_CREATE ioctl so that locks are assigned a bit later in the process. ==rob > > Best, > Jialin > Lawrence Berkeley Lab > > On Tue, Jan 12, 2016 at 11:22 AM, Rob Latham <robl(a)mcs.anl.gov > <mailto:[email protected]>> wrote: > > > > On 01/12/2016 11:36 AM, Jaln wrote: > > Hi, > I'm running hdft with mpiio on a single compute node (32 cores), 10 > OSTs, the file system is lustre v2.5. > I submit the job with 3 processes, they are writing to a shared > file, > which is about 3GBs, > and each process writes 1/3 of the file, for example, > The array is a 4D double array, 3*32*1024*128, then each process > writes > 32*1024*128 to the file, which is contiguous. > > I observed some wired performance number, I tried both > independent I/O > and collective IO. > In the case of independent I/O, each rank seems to block each > other and > finish writing one after another. But in collective I/O, all > three ranks > reports same I/O cost, I think this is because there is only one > aggregator. > My question is, in the case of independent I/O, are the I/Os > blocking > when accessing the file? > If not blocking, can I expect linear speedup on a single node by > increasing number of processes? > > > There is a lot going on under the hood in collective mode. Let's > start with independent mode. Here's my mental model of what's going on: > > - Your 3 process application issues 3 lustre writes. > - One of those will win the race to the file system, acquire a > whole-file lock, and begin to write. > - Now the request from the 2nd place process arrives. Lustre will > revoke the whole-file lock and issue a lock for the beginning of the > request to the end of the file. > - When the last process arrives, Lustre will revoke locks yet > again, and issue a lock from the beginning of the request to the end > of the file. > > So yep, there is indeed a lot of blocking going on. It's not a > formal queue, more of a side effect of waiting for the Lustre MDS to > issue the required locks. > > In collective I/O (which I'll assume is a relatively recent ROMIO > implementation), one of your three mpi processes will be the > aggregator. You seem to know about two-phase collective I/O so I > will make the rest of the explanation brief. Yes, that aggregator > will receive data from the other proceses and issue all I/O. The > other processes will wait until the aggregator finishes, which is > why you see all processes reporting the same run time for I/O. > > You are unlikely to get speedup from a single node for two main > reasons: There are the aforementioned lock contention issues. > There is a single link from that node to the 10 Lustre OSTs. > > In fact, due to the lock revocation activity I described above, you > are likely to see a massive performance crash when you involve a > second node. Then, as you add more nodes, you will finally light up > enough network links to see a speedup. > > ==rob > > > Best, > Jialin > Lawrence Berkeley Lab > > > _______________________________________________ > 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 <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > > -- > > Genius only means hard-working all one's life > > > > _______________________________________________ > 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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