October 2011 - moab-dev - mailman3.cels.anl.gov

r5199 - MOAB/trunk/src/io
by xbxu＠mcs.anl.gov 25 Oct '11

25 Oct '11

Author: xbxu Date: 2011-10-25 10:27:53 -0500 (Tue, 25 Oct 2011) New Revision: 5199 Modified: MOAB/trunk/src/io/ReadNC.cpp Log: remove reset method since the data member has already been initilized within the constructor initilizer list Modified: MOAB/trunk/src/io/ReadNC.cpp =================================================================== --- MOAB/trunk/src/io/ReadNC.cpp 2011-10-24 21:26:39 UTC (rev 5198) +++ MOAB/trunk/src/io/ReadNC.cpp 2011-10-25 15:27:53 UTC (rev 5199) @@ -39,8 +39,12 @@ #endif { assert(impl != NULL); - reset(); - + + for (unsigned int i = 0; i < 6; i++) { + gDims[i] = -1; + lDims[i] = -1; + } + impl->query_interface(readMeshIface); }

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r5198 - MOAB/trunk/test
by iulian＠mcs.anl.gov 24 Oct '11

24 Oct '11

Author: iulian Date: 2011-10-24 16:26:39 -0500 (Mon, 24 Oct 2011) New Revision: 5198 Modified: MOAB/trunk/test/Makefile.am Log: this typo was causing problems only for an out of source build (more exactly, during make check, kd_tree_test could not be compiled) Modified: MOAB/trunk/test/Makefile.am =================================================================== --- MOAB/trunk/test/Makefile.am 2011-10-24 03:31:07 UTC (rev 5197) +++ MOAB/trunk/test/Makefile.am 2011-10-24 21:26:39 UTC (rev 5198) @@ -125,7 +125,7 @@ if PARALLEL moab_test_CPPFLAGS += -I$(top_srcdir)/src/parallel -kd_tree_test_CPPFLAGS = -I$(top_srcdir)/src/parallel +kd_tree_test_CPPFLAGS += -I$(top_srcdir)/src/parallel test_prog_opt_CPPFLAGS += -I$(top_srcdir)/src/parallel endif

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r5197 - in MOAB/trunk/src/parallel: . moab
by hongjun＠mcs.anl.gov 23 Oct '11

23 Oct '11

Author: hongjun Date: 2011-10-23 22:31:07 -0500 (Sun, 23 Oct 2011) New Revision: 5197 Modified: MOAB/trunk/src/parallel/ParallelComm.cpp MOAB/trunk/src/parallel/moab/ParallelComm.hpp Log: o check and clean shared tags before exchange meshes o shared, multi-shared and pstatus are properly set and inserted to sharedEnts vector o passes make check Modified: MOAB/trunk/src/parallel/ParallelComm.cpp =================================================================== --- MOAB/trunk/src/parallel/ParallelComm.cpp 2011-10-22 22:09:34 UTC (rev 5196) +++ MOAB/trunk/src/parallel/ParallelComm.cpp 2011-10-24 03:31:07 UTC (rev 5197) @@ -5716,6 +5716,12 @@ exchange_procs_sets.push_back(exchange_procs[i]); } + // check and clean incorrect shared tags + result = clean_shared_tags(exchange_ents); + RRA("Couldn't clean shared tags."); + result = clean_shared_tags(exchange_sets); + RRA("Couldn't clean shared tags."); + // exchange entities first result = exchange_owned_mesh(exchange_procs, exchange_ents, store_remote_handles, wait_all, migrate); @@ -5728,6 +5734,53 @@ for (int i = 0; i < n_proc; i++) delete exchange_sets[i]; + // set shared information + Tag sharedp = sharedp_tag(); + Tag sharedps = sharedps_tag(); + Tag pstatus = pstatus_tag(); + Range tagged_ents; + + // get shared proc tag entities and add shared pstatus + result = mbImpl->get_entities_by_type_and_tag(0, MBMAXTYPE, &sharedp, 0, 1, + tagged_ents); + RRA("Failed to get sharing proc tag in remote_handles."); + + std::vector<int> shared_procs(tagged_ents.size()); + result = mbImpl->tag_get_data(sharedp, tagged_ents, &shared_procs[0]); + Range::iterator it = tagged_ents.begin(); + Range::iterator eit = tagged_ents.end(); + for (int i = 0; it != eit; it++, i++) { + unsigned char pstat; + pstat |= PSTATUS_SHARED; + result = mbImpl->tag_set_data(pstatus_tag(), &(*it), 1, &pstat); + RRA("Couldn't set pstatus tag."); + sharedEnts.push_back(*it); + } + + // get shared proc tag entities and add shared pstatus + tagged_ents.clear(); + result = mbImpl->get_entities_by_type_and_tag(0, MBMAXTYPE, &sharedps, 0, 1, + tagged_ents); + RRA("Failed to get sharing proc tag in remote_handles."); + + it = tagged_ents.begin();

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r5196 - MOAB/trunk/itaps/imesh
by tautges＠mcs.anl.gov 22 Oct '11

22 Oct '11

Author: tautges Date: 2011-10-22 17:09:34 -0500 (Sat, 22 Oct 2011) New Revision: 5196 Modified: MOAB/trunk/itaps/imesh/iMesh_f.h Log: Moving a #endif and include of iBase, was causing parameters in iBase_f.h to be undefined when a file included iMesh_f.h multiple times. Modified: MOAB/trunk/itaps/imesh/iMesh_f.h =================================================================== --- MOAB/trunk/itaps/imesh/iMesh_f.h 2011-10-19 01:33:03 UTC (rev 5195) +++ MOAB/trunk/itaps/imesh/iMesh_f.h 2011-10-22 22:09:34 UTC (rev 5196) @@ -1,12 +1,14 @@ #ifndef IMESH_F_H #define IMESH_F_H -#include "iBase_f.h" - #define iMesh_Instance IBASE_HANDLE_T #define iBase_EntityIterator IBASE_HANDLE_T #define iBase_EntityArrIterator IBASE_HANDLE_T +#endif + +#include "iBase_f.h" + integer iMesh_POINT integer iMesh_LINE_SEGMENT integer iMesh_POLYGON @@ -45,4 +47,3 @@ parameter (iMesh_GLOBAL_TRAVERSAL = 3) -#endif

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moab::ReadUtilIface
by Iulian Grindeanu 19 Oct '11

19 Oct '11

Hello, I have a question about the difference in create_element and ReadUtilIFace. we use ReadUtilIFace in MeshKit to create new element meshes. It is more efficient, but there is drawback; the adjacency is not recomputed for the new elements; there is no notification sent to AEntityFactory to update adjacency for newly created elements (like the one in ErrorCode Core::create_element(const EntityType type, const EntityHandle *connectivity, const int num_nodes, EntityHandle &handle)) What is the correct way of doing it? If we need adjacency? In my scenario, I created new triangles, but after that, I needed the Skinner. It failed, because there were no adjacencies between new nodes and new triangles. I can always change the code to use "create_element", but is there a way to force recomputation of adjacencies after using ReadUtilIFace? Thanks, Iulian

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r5195 - MOAB/trunk/src/parallel
by jain＠mcs.anl.gov 18 Oct '11

18 Oct '11

Author: jain Date: 2011-10-18 20:33:03 -0500 (Tue, 18 Oct 2011) New Revision: 5195 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: o Fix bug for in communicate shared sets when non-blocking recv for small buffer consumes the data for large buffers. o Added a new variable lrecv_req for large buffer. Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-10-13 21:56:23 UTC (rev 5194) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-10-19 01:33:03 UTC (rev 5195) @@ -1836,7 +1836,9 @@ // post receive buffers for all owned sets for all sharing procs - std::vector<MPI_Request> recv_req(numrecv); + std::vector<MPI_Request> recv_req(numrecv, MPI_REQUEST_NULL); + std::vector<MPI_Request> lrecv_req(numrecv, MPI_REQUEST_NULL); + std::vector< std::vector<unsigned long> > recv_buf(numrecv,std::vector<unsigned long>(init_buff_size)); int idx = 0; for (Range::iterator i = owned.begin(); i != owned.end(); ++i) { @@ -1952,7 +1954,6 @@ rval = unpack_set( handle, &buff[0], init_buff_size ); CHECK_MB(rval); dead.swap(buff); // release memory - recv_req[idx] = MPI_REQUEST_NULL; } else { // data was too big for init_buff_size @@ -1961,11 +1962,11 @@ dbgOut.printf(5,"Re-Posting buffer to receive set %d from proc %d with size %lu\n", status.MPI_TAG, status.MPI_SOURCE, (unsigned long)size ); mperr = MPI_Irecv( &buff[0], size, MPI_UNSIGNED_LONG, status.MPI_SOURCE, - status.MPI_TAG, comm, &recv_req[idx] ); + status.MPI_TAG, comm, &lrecv_req[idx] ); CHECK_MPI(mperr); ++numrecv; } - //recv_req[idx] = MPI_REQUEST_NULL; + recv_req[idx] = MPI_REQUEST_NULL; } @@ -2000,7 +2001,7 @@ while (remaining--) { std::vector<unsigned long> dead; MPI_Status status; - mperr = MPI_Waitany( recv_req.size(), &recv_req[0], &idx, &status ); + mperr = MPI_Waitany( lrecv_req.size(), &lrecv_req[0], &idx, &status ); CHECK_MPI(mperr); EntityHandle handle = CREATE_HANDLE( MBENTITYSET, status.MPI_TAG ); std::vector<unsigned long>& buff = recv_buf[idx]; @@ -2010,7 +2011,7 @@ CHECK_MB(rval); dead.swap(buff); // release memory - recv_req[idx] = MPI_REQUEST_NULL;

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Re: [MOAB-dev] moab-announce Digest, Vol 5, Issue 2
by Hong-Jun Kim 13 Oct '11

13 Oct '11

Revision 5195 from Jane solves your problem. Please update and recompile the code. Thank you, Jain. Hong-Jun ----- Original Message ----- > From: "Tiantian Xu" <tiantianxu.88(a)gmail.com> > To: "Hong-Jun Kim" <hongjun(a)mcs.anl.gov> > Sent: Thursday, October 13, 2011 2:22:00 PM > Subject: Re: moab-announce Digest, Vol 5, Issue 2 > Yes, I enabled parallel when building HDF5. There is a test file > "ph5example.c" in the HDF5 source code to test HDF5 parallel > operations, it runs correctly so I think HDF5 library is good. Tests > in netcdf "make check" are all passed, so netcdf should be good too, > unless there are some hidden problems... > Thanks! > > Tiantian > > > On Thu, Oct 13, 2011 at 2:47 PM, Hong-Jun Kim < hongjun(a)mcs.anl.gov > > wrote: > > > I am checking it, before that, are you using a parallel build of the > HDF5 library? > Thanks. > > Hong-Jun > > > > > > ----- Original Message ----- > > From: "Tiantian Xu" < tiantianxu.88(a)gmail.com > > > To: "Hong-Jun Kim" < hongjun(a)mcs.anl.gov > > > Sent: Thursday, October 13, 2011 12:11:09 PM > > Subject: Re: moab-announce Digest, Vol 5, Issue 2 > > Hi Hong-Jun, > > > > Yes, that machine is 64bit, however the Fedora installed is a 32-bit > > version, I'm not sure if this is the problem... However I have > > decided > > not to dig into the problem on that machine any more... > > I had reinstalled hdf5 and netcdf on a different machine, also 64 > > bit, > > with 64-bit Fedora. Moab "configure", "make", "make check" and "make > > install" were all successful. But the same error in parallel read > > occurred: > > > > [tiantian@vis-pc2 bin]$ mpiexec -np 2 ./mbconvert -O > > PARALLEL=READ_PART -O PARTITION=MATERIAL_SET -O > > PARALLEL_RESOLVE_SHARED_ENTS -O PARALLEL_GHOSTS=3.0.1 -o > > PARALLEL=WRITE_PART ./64bricks_512hex.h5m dummy.h5m > > Read "./64bricks_512hex.h5m" > > > > ===================================================================================== > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = EXIT CODE: 139 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > ===================================================================================== > > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > > (signal 11) > > > > I'm very confused because now the "make check" works, all tests are > > passed, same error still occurs. So it is very likely that there are > > some subtle issues... > > The config and make log from the installed lib directory are > > attached. > > > > Thank you so much for the help. > > > > Tiantian > > > > > > On Thu, Oct 13, 2011 at 11:33 AM, Hong-Jun Kim < hongjun(a)mcs.anl.gov > > > > > wrote: > > > > > > Actually, I can not replicate the problem in my machine. > > Can you check if your machine is 64bit with "uname -m" command? > > > > Could anyone have any idea about the question below? > > Can "netcdf-4" disabled netcdf cause any segmentation error? > > > > > > > Also, before I built MOAB, when I was trying to build netcdf, > > > configure complained it could not find the z library, so I turned > > > off > > > "netcdf-4" feature, in other words, the netcdf library was not > > > built > > > on top of hdf5/zlib. Could this be the problem? > > > > Thanks. > > > > Hong-Jun > > > > > > > > > > > > > Hi Hong-Jun, > > > > > > I still have the same problems after chaning "LFLAGS=-static". > > > "config.log", "mbcn_test.log" and "test-suite.log" are all > > > attached. > > > But I'm not sure what you mean by "error signs".. > > > Also, before I built MOAB, when I was trying to build netcdf, > > > configure complained it could not find the z library, so I turned > > > off > > > "netcdf-4" feature, in other words, the netcdf library was not > > > built > > > on top of hdf5/zlib. Could this be the problem? I'm still trying > > > to > > > fix the "can't find z lib" error with netcdf. > > > > > > Thanks for your help! > > > > > > Tiantian > > > > > > > > > On Wed, Oct 12, 2011 at 1:19 PM, Hong-Jun Kim < > > > hongjun(a)mcs.anl.gov > > > > > > > wrote: > > > > > > > > > If you still have the same problems with Tim's suggestion as > > > below, > > > could you please send me your "config.log" and error signs for me > > > to > > > replicate it? > > > > > > In addition, can you use " moab-dev(a)mcs.anl.gov " for this kind of > > > question? > > > "moab-announce" is for announcing new things and upgrades and > > > looks > > > it > > > has some latencies to get mail.(I just got Tim's message which > > > looks > > > sent yesterday) > > > > > > Thanks. > > > > > > ----------------------------- > > > Hong-Jun Kim > > > Post-doc researcher > > > MCS, Argonne National Laboratory > > > 9700 S. Cass Ave. B240/R2147 > > > Argonne, IL 60439 > > > 630-252-4791 > > > hongjun(a)mcs.anl.gov > > > ----------------------------- > > > > > > > Hong-Jun, > > > > Can you check this out? Tiantian, we haven't seen this problem > > > > anywhere. The output from your configure looks like > > > > you're on a 64bit machine, but can you verify that? The only > > > > other > > > > thing that looks strange in your configure is the > > > > LFLAGS=-static; you should be able to get the same thing, in a > > > > more > > > > standard way, using --disable-shared > > > > --enable-static. Could you try that? Thanks. > > > > > > > > - tim > > > > > > > > On 10/11/2011 12:58 PM, Tiantian Xu wrote: > > > > > > > > > > Hi, > > > > > > > > > > I was trying to build moab but met with the "mbcn_test fail" > > > > > during > > > > > make > > > > > check. > > > > > The commands I used to build the library were: > > > > > > > > > > ./configure LFLAGS=-static > > > > > --with-mpi=/home/tiantian/ITL/mpich2-1.4.1p1/gcc > > > > > --with-hdf5=/home/tiantian/hdf5 > > > > > --with-netcdf=/home/tiantian/ITL/netcdf-4.1.3/gcc > > > > > --with-zlib=/home/tiantian/ITL/zlib-1.2.5/gcc > > > > > --with-szip=/home/tiantian/ITL/szip-2.1/gcc > > > > > --prefix=/home/tiantian/ITL/moab 2>&1 | tee configure.log > > > > > make 2>&1 | make.log > > > > > make check 2>&1 | tee make.check.log > > > > > > > > > > Looks like the mbcn_test is about query on entities, I don't > > > > > know > > > > > why > > > > > this went wrong. Later I ignored the make check errors and did > > > > > "make > > > > > install". I tried to perform parallel read/write and found > > > > > mbconvert > > > > > went wrong too: > > > > > > > > > > $mpiexec -np 2 ./mbconvert -O PARALLEL=READ_PART -O > > > > > PARTITION=MATERIAL_SET -O PARALLEL_RESOLVE_SHARED_ENTS -O > > > > > PARALLEL_GHOSTS=3.0.1 -o PARALLEL=WRITE_PART > > > > > ./64bricks_512hex.h5m > > > > > dummy.h5m > > > > > Read "./64bricks_512hex.h5m" > > > > > > > > > > ===================================================================================== > > > > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > > > > = EXIT CODE: 139 > > > > > = CLEANING UP REMAINING PROCESSES > > > > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > > > > ===================================================================================== > > > > > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation > > > > > fault > > > > > (signal 11) > > > > > > > > > > I suspect some fundamental functions in moab were not properly > > > > > made? > > > > > I had attached the log files. Please take a look. > > > > > > > > > > Thanks a lot for your help! > > > > > > > > > > Best, > > > > > Tiantian > > > > > > > > > > > > > -- > > > > ================================================================ > > > > "You will keep in perfect peace him whose mind is > > > > steadfast, because he trusts in you." Isaiah 26:3 > > > > > > > > Tim Tautges Argonne National Laboratory > > > > ( tautges(a)mcs.anl.gov ) (telecommuting from UW-Madison) > > > > > > > > > > phone: (608) 263-8485 1500 Engineering Dr. > > > > fax: (608) 263-4499 Madison, WI 53706 > > > > > > > > > > > > > > > > ------------------------------ > > > > > > > > _______________________________________________ > > > > moab-announce mailing list > > > > moab-announce(a)mcs.anl.gov > > > > https://lists.mcs.anl.gov/mailman/listinfo/moab-announce > > > > > > > > > > > > End of moab-announce Digest, Vol 5, Issue 2 > > > > *******************************************

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r5194 - MOAB/trunk/src/parallel
by jain＠mcs.anl.gov 13 Oct '11

13 Oct '11

Author: jain Date: 2011-10-13 16:56:23 -0500 (Thu, 13 Oct 2011) New Revision: 5194 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: Fix bug in resolve shared set data Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-10-13 15:51:48 UTC (rev 5193) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-10-13 21:56:23 UTC (rev 5194) @@ -1952,6 +1952,7 @@ rval = unpack_set( handle, &buff[0], init_buff_size ); CHECK_MB(rval); dead.swap(buff); // release memory + recv_req[idx] = MPI_REQUEST_NULL; } else { // data was too big for init_buff_size @@ -1963,9 +1964,8 @@ status.MPI_TAG, comm, &recv_req[idx] ); CHECK_MPI(mperr); ++numrecv; - } - - recv_req[idx] = MPI_REQUEST_NULL; + } + //recv_req[idx] = MPI_REQUEST_NULL; }

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Re: [MOAB-dev] moab-announce Digest, Vol 5, Issue 2
by Hong-Jun Kim 13 Oct '11

13 Oct '11

I am checking it, before that, are you using a parallel build of the HDF5 library? Thanks. Hong-Jun ----- Original Message ----- > From: "Tiantian Xu" <tiantianxu.88(a)gmail.com> > To: "Hong-Jun Kim" <hongjun(a)mcs.anl.gov> > Sent: Thursday, October 13, 2011 12:11:09 PM > Subject: Re: moab-announce Digest, Vol 5, Issue 2 > Hi Hong-Jun, > > Yes, that machine is 64bit, however the Fedora installed is a 32-bit > version, I'm not sure if this is the problem... However I have decided > not to dig into the problem on that machine any more... > I had reinstalled hdf5 and netcdf on a different machine, also 64 bit, > with 64-bit Fedora. Moab "configure", "make", "make check" and "make > install" were all successful. But the same error in parallel read > occurred: > > [tiantian@vis-pc2 bin]$ mpiexec -np 2 ./mbconvert -O > PARALLEL=READ_PART -O PARTITION=MATERIAL_SET -O > PARALLEL_RESOLVE_SHARED_ENTS -O PARALLEL_GHOSTS=3.0.1 -o > PARALLEL=WRITE_PART ./64bricks_512hex.h5m dummy.h5m > Read "./64bricks_512hex.h5m" > > ===================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 139 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > ===================================================================================== > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > (signal 11) > > I'm very confused because now the "make check" works, all tests are > passed, same error still occurs. So it is very likely that there are > some subtle issues... > The config and make log from the installed lib directory are attached. > > Thank you so much for the help. > > Tiantian > > > On Thu, Oct 13, 2011 at 11:33 AM, Hong-Jun Kim < hongjun(a)mcs.anl.gov > > wrote: > > > Actually, I can not replicate the problem in my machine. > Can you check if your machine is 64bit with "uname -m" command? > > Could anyone have any idea about the question below? > Can "netcdf-4" disabled netcdf cause any segmentation error? > > > > Also, before I built MOAB, when I was trying to build netcdf, > > configure complained it could not find the z library, so I turned > > off > > "netcdf-4" feature, in other words, the netcdf library was not built > > on top of hdf5/zlib. Could this be the problem? > > Thanks. > > Hong-Jun > > > > > > > Hi Hong-Jun, > > > > I still have the same problems after chaning "LFLAGS=-static". > > "config.log", "mbcn_test.log" and "test-suite.log" are all attached. > > But I'm not sure what you mean by "error signs".. > > Also, before I built MOAB, when I was trying to build netcdf, > > configure complained it could not find the z library, so I turned > > off > > "netcdf-4" feature, in other words, the netcdf library was not built > > on top of hdf5/zlib. Could this be the problem? I'm still trying to > > fix the "can't find z lib" error with netcdf. > > > > Thanks for your help! > > > > Tiantian > > > > > > On Wed, Oct 12, 2011 at 1:19 PM, Hong-Jun Kim < hongjun(a)mcs.anl.gov > > > > > wrote: > > > > > > If you still have the same problems with Tim's suggestion as below, > > could you please send me your "config.log" and error signs for me to > > replicate it? > > > > In addition, can you use " moab-dev(a)mcs.anl.gov " for this kind of > > question? > > "moab-announce" is for announcing new things and upgrades and looks > > it > > has some latencies to get mail.(I just got Tim's message which looks > > sent yesterday) > > > > Thanks. > > > > ----------------------------- > > Hong-Jun Kim > > Post-doc researcher > > MCS, Argonne National Laboratory > > 9700 S. Cass Ave. B240/R2147 > > Argonne, IL 60439 > > 630-252-4791 > > hongjun(a)mcs.anl.gov > > ----------------------------- > > > > > Hong-Jun, > > > Can you check this out? Tiantian, we haven't seen this problem > > > anywhere. The output from your configure looks like > > > you're on a 64bit machine, but can you verify that? The only other > > > thing that looks strange in your configure is the > > > LFLAGS=-static; you should be able to get the same thing, in a > > > more > > > standard way, using --disable-shared > > > --enable-static. Could you try that? Thanks. > > > > > > - tim > > > > > > On 10/11/2011 12:58 PM, Tiantian Xu wrote: > > > > > > > > Hi, > > > > > > > > I was trying to build moab but met with the "mbcn_test fail" > > > > during > > > > make > > > > check. > > > > The commands I used to build the library were: > > > > > > > > ./configure LFLAGS=-static > > > > --with-mpi=/home/tiantian/ITL/mpich2-1.4.1p1/gcc > > > > --with-hdf5=/home/tiantian/hdf5 > > > > --with-netcdf=/home/tiantian/ITL/netcdf-4.1.3/gcc > > > > --with-zlib=/home/tiantian/ITL/zlib-1.2.5/gcc > > > > --with-szip=/home/tiantian/ITL/szip-2.1/gcc > > > > --prefix=/home/tiantian/ITL/moab 2>&1 | tee configure.log > > > > make 2>&1 | make.log > > > > make check 2>&1 | tee make.check.log > > > > > > > > Looks like the mbcn_test is about query on entities, I don't > > > > know > > > > why > > > > this went wrong. Later I ignored the make check errors and did > > > > "make > > > > install". I tried to perform parallel read/write and found > > > > mbconvert > > > > went wrong too: > > > > > > > > $mpiexec -np 2 ./mbconvert -O PARALLEL=READ_PART -O > > > > PARTITION=MATERIAL_SET -O PARALLEL_RESOLVE_SHARED_ENTS -O > > > > PARALLEL_GHOSTS=3.0.1 -o PARALLEL=WRITE_PART > > > > ./64bricks_512hex.h5m > > > > dummy.h5m > > > > Read "./64bricks_512hex.h5m" > > > > > > > > ===================================================================================== > > > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > > > = EXIT CODE: 139 > > > > = CLEANING UP REMAINING PROCESSES > > > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > > > ===================================================================================== > > > > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > > > > (signal 11) > > > > > > > > I suspect some fundamental functions in moab were not properly > > > > made? > > > > I had attached the log files. Please take a look. > > > > > > > > Thanks a lot for your help! > > > > > > > > Best, > > > > Tiantian > > > > > > > > > > -- > > > ================================================================ > > > "You will keep in perfect peace him whose mind is > > > steadfast, because he trusts in you." Isaiah 26:3 > > > > > > Tim Tautges Argonne National Laboratory > > > ( tautges(a)mcs.anl.gov ) (telecommuting from UW-Madison) > > > > > > phone: (608) 263-8485 1500 Engineering Dr. > > > fax: (608) 263-4499 Madison, WI 53706 > > > > > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > moab-announce mailing list > > > moab-announce(a)mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/moab-announce > > > > > > > > > End of moab-announce Digest, Vol 5, Issue 2 > > > *******************************************

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Re: [MOAB-dev] moab-announce Digest, Vol 5, Issue 2
by Hong-Jun Kim 13 Oct '11

13 Oct '11

Actually, I can not replicate the problem in my machine. Can you check if your machine is 64bit with "uname -m" command? Could anyone have any idea about the question below? Can "netcdf-4" disabled netcdf cause any segmentation error? > Also, before I built MOAB, when I was trying to build netcdf, > configure complained it could not find the z library, so I turned off > "netcdf-4" feature, in other words, the netcdf library was not built > on top of hdf5/zlib. Could this be the problem? Thanks. Hong-Jun > Hi Hong-Jun, > > I still have the same problems after chaning "LFLAGS=-static". > "config.log", "mbcn_test.log" and "test-suite.log" are all attached. > But I'm not sure what you mean by "error signs".. > Also, before I built MOAB, when I was trying to build netcdf, > configure complained it could not find the z library, so I turned off > "netcdf-4" feature, in other words, the netcdf library was not built > on top of hdf5/zlib. Could this be the problem? I'm still trying to > fix the "can't find z lib" error with netcdf. > > Thanks for your help! > > Tiantian > > > On Wed, Oct 12, 2011 at 1:19 PM, Hong-Jun Kim < hongjun(a)mcs.anl.gov > > wrote: > > > If you still have the same problems with Tim's suggestion as below, > could you please send me your "config.log" and error signs for me to > replicate it? > > In addition, can you use " moab-dev(a)mcs.anl.gov " for this kind of > question? > "moab-announce" is for announcing new things and upgrades and looks it > has some latencies to get mail.(I just got Tim's message which looks > sent yesterday) > > Thanks. > > ----------------------------- > Hong-Jun Kim > Post-doc researcher > MCS, Argonne National Laboratory > 9700 S. Cass Ave. B240/R2147 > Argonne, IL 60439 > 630-252-4791 > hongjun(a)mcs.anl.gov > ----------------------------- > > > Hong-Jun, > > Can you check this out? Tiantian, we haven't seen this problem > > anywhere. The output from your configure looks like > > you're on a 64bit machine, but can you verify that? The only other > > thing that looks strange in your configure is the > > LFLAGS=-static; you should be able to get the same thing, in a more > > standard way, using --disable-shared > > --enable-static. Could you try that? Thanks. > > > > - tim > > > > On 10/11/2011 12:58 PM, Tiantian Xu wrote: > > > > > > Hi, > > > > > > I was trying to build moab but met with the "mbcn_test fail" > > > during > > > make > > > check. > > > The commands I used to build the library were: > > > > > > ./configure LFLAGS=-static > > > --with-mpi=/home/tiantian/ITL/mpich2-1.4.1p1/gcc > > > --with-hdf5=/home/tiantian/hdf5 > > > --with-netcdf=/home/tiantian/ITL/netcdf-4.1.3/gcc > > > --with-zlib=/home/tiantian/ITL/zlib-1.2.5/gcc > > > --with-szip=/home/tiantian/ITL/szip-2.1/gcc > > > --prefix=/home/tiantian/ITL/moab 2>&1 | tee configure.log > > > make 2>&1 | make.log > > > make check 2>&1 | tee make.check.log > > > > > > Looks like the mbcn_test is about query on entities, I don't know > > > why > > > this went wrong. Later I ignored the make check errors and did > > > "make > > > install". I tried to perform parallel read/write and found > > > mbconvert > > > went wrong too: > > > > > > $mpiexec -np 2 ./mbconvert -O PARALLEL=READ_PART -O > > > PARTITION=MATERIAL_SET -O PARALLEL_RESOLVE_SHARED_ENTS -O > > > PARALLEL_GHOSTS=3.0.1 -o PARALLEL=WRITE_PART ./64bricks_512hex.h5m > > > dummy.h5m > > > Read "./64bricks_512hex.h5m" > > > > > > ===================================================================================== > > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > > = EXIT CODE: 139 > > > = CLEANING UP REMAINING PROCESSES > > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > > ===================================================================================== > > > APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault > > > (signal 11) > > > > > > I suspect some fundamental functions in moab were not properly > > > made? > > > I had attached the log files. Please take a look. > > > > > > Thanks a lot for your help! > > > > > > Best, > > > Tiantian > > > > > > > -- > > ================================================================ > > "You will keep in perfect peace him whose mind is > > steadfast, because he trusts in you." Isaiah 26:3 > > > > Tim Tautges Argonne National Laboratory > > ( tautges(a)mcs.anl.gov ) (telecommuting from UW-Madison) > > phone: (608) 263-8485 1500 Engineering Dr. > > fax: (608) 263-4499 Madison, WI 53706 > > > > > > > > ------------------------------ > > > > _______________________________________________ > > moab-announce mailing list > > moab-announce(a)mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/moab-announce > > > > > > End of moab-announce Digest, Vol 5, Issue 2 > > *******************************************

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