November 2012 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Use of MPI derived data types / MPI file IO
by jgrime＠uchicago.edu 18 Nov '12

18 Nov '12

Hi Wei-keng, That's a good point, thanks! However, I actually only want to save certain parts of the "atom" structure to file, and saving the whole array as a raw dump could waste a lot of disk space. For example, the "atom" structure I used in the example code in reality contains not only an integer and three contiguous doubles, but also at least another two double[3] entries which I may not want to save to disk. As the full data set can be hundreds of millions (or even billions) of "atom" structures, using a derived data type with only a restricted subset of the data in each "atom" structure will produce considerably smaller file sizes! There's also the problem of making the resultant file "portable" - raw memory dumps could make life difficult in trying to use output files on machines with different processor architectures. Once I get the derived data types working, I can then switch from the "native" representation to something else ("external32" etc), which should allow me to create portable output files, provided I'm careful with using MPIs file offset routines etc if the file is larger than plain old 32 bit offsets can handle. Cheers, J. ---- Original message ---- >Date: Sun, 18 Nov 2012 12:27:04 -0600 >From: discuss-bounces(a)mpich.org (on behalf of Wei-keng Liao <wkliao(a)ece.northwestern.edu>) >Subject: Re: [mpich-discuss] Use of MPI derived data types / MPI file IO >To: discuss(a)mpich.org > >Hi, John > >If your I/O is simply appending one process's data after another and the I/O buffers in memory >are all contiguous, then you can simply do the following without defining MPI >derived data types or setting the file view. > >MPI_File_write_at_all(f, offset, &atoms[0], (int)atoms.size() * sizeof(struct atom), MPI_BYTE, &stat); > >Using derived data types is usually when you have noncontiguous buffer in memory or >want to access non-contiguous data in files. > > >Wei-keng > >On Nov 18, 2012, at 11:52 AM, <jgrime(a)uchicago.edu> <jgrime(a)uchicago.edu> wrote: > >> Hi all, >> >> I'm having some problems with using derived data types and MPI parallel IO, and >> was wondering if anyone could help. I tried to search the archives in case this >> was covered earlier, but that just gave me "ht://Dig error" messages. >> >> Outline: I have written a C++ program where each MPI rank acts on data stored >> in a local array of structures. The arrays are typically of different lengths on each >> rank. I wish to write and read the contents of these arrays to disk using MPI's >> parallel IO routines. The file format is simply an initial integer which describes >> how many "structures" are in the file, followed by the data which represents the >> "structure information" from all ranks (ie the total data set). >> >> So far, I've tried two different approaches: the first consists of each rank >> serialising the contents of the local array of structures into a byte array, which is >> then saved to file "f" using MPI_File_set_view( f, MPI_COMM_WORLD, offset, >> MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL ) to skip the initial integer >> "header" and then a call to MPI_File_write_all( f, local_bytearray, local_n_bytes, >> MPI_CHAR, &status ). Here, "offset" is simply the size of an integer (in bytes) + >> the summation of the number of bytes each preceeding rank wishes to write to >> the file (received via an earlier MPI_Allgather call). This seems to work, as when I >> read the file back in on a single MPI rank and deserialise the data into an array of >> structures I get the results I expect. >> >> The second approach is to use MPI's derived data types to create MPI >> representations of the structures, and then treat the arrays of structures as MPI >> data types. This allows me to avoid copying the local data into an intermediate >> buffer etc, and seems the more elegant approach. I cannot, however, seem to >> make this approach work. >> >> I'm pretty sure the problem lies in my use of the file views, but I'm not sure >> where I'm going wrong. The reading of the integer "header" always works fine, >> but the proceeding data is garbled. I'm using the "native" data representation for >> testing, but will likely change that to something more portable when I get this >> code working. >> >> I've included the important excerpts of the test code I'm trying to use below >> (with some printf()s and error handling etc removed to make it a little more >> concise). I have previously tested that std::vector allocates a contiguous flat >> array of the appropriate data type in memory, so passing a pointer/reference to >> the first element in such a data structure behaves the same way as simply >> passing a conventional array of the appropriate data type: >> >> struct atom >> { >> int global_id; >> double xyz[3]; >> }; >> >> void write( char * fpath, std::vector<struct atom> &atoms, int rank, int nranks ) >> { >> /* >> Memory layout information for the structure we wish to convert into >> an >> MPI derived data type. >> */ >> std::vector<int> s_blocklengths; >> std::vector<MPI_Aint> s_displacements; >> std::vector<MPI_Datatype> s_datatypes; >> MPI_Aint addr_start, addr; >> MPI_Datatype mpi_atom_type, mpi_atom_type_resized; >> int type_size; >> >> struct atom a; >> >> MPI_File f; >> MPI_Status stat; >> MPI_Offset offset; >> char *datarep = (char *)"native"; >> >> std::vector<int> all_N; >> int local_N, global_N; >> >> /* >> Set up the structure data type: single integer, and 3 double precision >> floats. >> We use the temporary "a" structure to determine the layout of memory >> inside >> atom structures. >> */ >> MPI_Get_address( &a, &addr_start ); >> >> s_blocklengths.push_back( 1 ); >> s_datatypes.push_back( MPI_INT ); >> MPI_Get_address( &a.global_id, &addr ); >> s_displacements.push_back( addr - addr_start ); >> >> s_blocklengths.push_back( 3 ); >> s_datatypes.push_back( MPI_DOUBLE ); >> MPI_Get_address( &a.xyz[0], &addr ); >> s_displacements.push_back( addr - addr_start ); >> >> MPI_Type_create_struct( (int)s_blocklengths.size(), &s_blocklengths[0], >> &s_displacements[0], &s_datatypes[0], &mpi_atom_type ); >> MPI_Type_commit( &mpi_atom_type ); >> >> /* >> Take into account any compiler padding in creating an array of >> structures. >> */ >> MPI_Type_create_resized( mpi_atom_type, 0, sizeof(struct atom), >> &mpi_atom_type_resized ); >> MPI_Type_commit( &mpi_atom_type_resized ); >> >> MPI_Type_size( mpi_atom_type_resized, &type_size ); >> >> local_N = (int)atoms.size(); >> all_N.resize( nranks ); >> >> MPI_Allgather( &local_N, 1, MPI_INT, &all_N[0], 1, MPI_INT, >> MPI_COMM_WORLD ); >> >> global_N = 0; >> for( size_t i=0; i<all_N.size(); i++ ) global_N += all_N[i]; >> >> offset = 0; >> for( int i=0; i<rank; i++ ) offset += all_N[i]; >> >> offset *= type_size; // convert from structure counts -> bytes into file for >> true structure size >> offset += sizeof( int ); // skip leading integer (global_N) in file. >> >> MPI_File_open( MPI_COMM_WORLD, fpath, MPI_MODE_CREATE | >> MPI_MODE_WRONLY, MPI_INFO_NULL, &f ); >> if( rank == 0 ) >> { >> MPI_File_write( f, &global_N, 1, MPI_INT, &stat ); >> } >> MPI_File_set_view( f, offset, mpi_atom_type_resized, >> mpi_atom_type_resized, datarep, MPI_INFO_NULL ); >> >> MPI_File_write_all( f, &atoms[0], (int)atoms.size(), mpi_atom_type_resized, >> &stat ); >> MPI_File_close( &f ); >> >> MPI_Type_free( &mpi_atom_type ); >> MPI_Type_free( &mpi_atom_type_resized ); >> >> return; >> } >> >> void read( char * fpath, std::vector<struct atom> &atoms ) >> { >> std::vector<int> s_blocklengths; >> std::vector<MPI_Aint> s_displacements; >> std::vector<MPI_Datatype> s_datatypes; >> MPI_Datatype mpi_atom_type, mpi_atom_type_resized; >> >> struct atom a; >> MPI_Aint addr_start, addr; >> >> MPI_File f; >> MPI_Status stat; >> >> int global_N; >> char *datarep = (char *)"native"; >> >> int type_size; >> >> /* >> Set up the structure data type >> */ >> MPI_Get_address( &a, &addr_start ); >> >> s_blocklengths.push_back( 1 ); >> s_datatypes.push_back( MPI_INT ); >> MPI_Get_address( &a.global_id, &addr ); >> s_displacements.push_back( addr - addr_start ); >> >> s_blocklengths.push_back( 3 ); >> s_datatypes.push_back( MPI_DOUBLE ); >> MPI_Get_address( &a.xyz[0], &addr ); >> s_displacements.push_back( addr - addr_start ); >> >> MPI_Type_create_struct( (int)s_blocklengths.size(), &s_blocklengths[0], >> &s_displacements[0], &s_datatypes[0], &mpi_atom_type ); >> MPI_Type_commit( &mpi_atom_type ); >> >> /* >> Take into account any compiler padding in creating an array of >> structures. >> */ >> MPI_Type_create_resized( mpi_atom_type, 0, sizeof(struct atom), >> &mpi_atom_type_resized ); >> MPI_Type_commit( &mpi_atom_type_resized ); >> >> MPI_Type_size( mpi_atom_type_resized, &type_size ); >> >> MPI_File_open( MPI_COMM_SELF, fpath, MPI_MODE_RDONLY, >> MPI_INFO_NULL, &f ); >> >> MPI_File_read( f, &global_N, 1, MPI_INT, &stat ); >> >> atoms.clear(); >> atoms.resize( global_N ); >> >> errcode = MPI_File_set_view( f, sizeof(int), mpi_atom_type_resized, >> mpi_atom_type_resized, datarep, MPI_INFO_NULL ); >> errcode = MPI_File_read( f, &atoms[0], global_N, mpi_atom_type_resized, >> &stat ); >> errcode = MPI_File_close( &f ); >> >> MPI_Type_free( &mpi_atom_type ); >> MPI_Type_free( &mpi_atom_type_resized ); >> >> return; >> } >> >> Calling MPI_Type_get_extent() and MPI_Type_get_true_extent() for both >> mpi_atom_type and mpi_atom_type_resized returns (0,32) bytes in all cases. >> Calling MPI_Type_size() on both derived data types returns 28 bytes. >> >> If I call MPI_File_get_type_extent() on both derived data types after opening the >> file, they both resolve to 32 bytes - so I think the problem is in the difference >> between the data representation in memory and on disk. If I explicitly use 32 >> bytes in the offset calculation in the write() routine above, it still doesn't work. >> >> I'm finding it remarkably difficult to do something very simple using MPI's >> derived data types and the parallel IO, and hence I'm guessing that I have >> fundamentally misunderstood one or more aspects of this. If anyone can help >> clarify where I'm going wrong, that would be much appreciated! >> >> Cheers, >> >> John. >> _______________________________________________ >> 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] Use of MPI derived data types / MPI file IO
by Wei-keng Liao 18 Nov '12

18 Nov '12

Hi, John If your I/O is simply appending one process's data after another and the I/O buffers in memory are all contiguous, then you can simply do the following without defining MPI derived data types or setting the file view. MPI_File_write_at_all(f, offset, &atoms[0], (int)atoms.size() * sizeof(struct atom), MPI_BYTE, &stat); Using derived data types is usually when you have noncontiguous buffer in memory or want to access non-contiguous data in files. Wei-keng On Nov 18, 2012, at 11:52 AM, <jgrime(a)uchicago.edu> <jgrime(a)uchicago.edu> wrote: > Hi all, > > I'm having some problems with using derived data types and MPI parallel IO, and > was wondering if anyone could help. I tried to search the archives in case this > was covered earlier, but that just gave me "ht://Dig error" messages. > > Outline: I have written a C++ program where each MPI rank acts on data stored > in a local array of structures. The arrays are typically of different lengths on each > rank. I wish to write and read the contents of these arrays to disk using MPI's > parallel IO routines. The file format is simply an initial integer which describes > how many "structures" are in the file, followed by the data which represents the > "structure information" from all ranks (ie the total data set). > > So far, I've tried two different approaches: the first consists of each rank > serialising the contents of the local array of structures into a byte array, which is > then saved to file "f" using MPI_File_set_view( f, MPI_COMM_WORLD, offset, > MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL ) to skip the initial integer > "header" and then a call to MPI_File_write_all( f, local_bytearray, local_n_bytes, > MPI_CHAR, &status ). Here, "offset" is simply the size of an integer (in bytes) + > the summation of the number of bytes each preceeding rank wishes to write to > the file (received via an earlier MPI_Allgather call). This seems to work, as when I > read the file back in on a single MPI rank and deserialise the data into an array of > structures I get the results I expect. > > The second approach is to use MPI's derived data types to create MPI > representations of the structures, and then treat the arrays of structures as MPI > data types. This allows me to avoid copying the local data into an intermediate > buffer etc, and seems the more elegant approach. I cannot, however, seem to > make this approach work. > > I'm pretty sure the problem lies in my use of the file views, but I'm not sure > where I'm going wrong. The reading of the integer "header" always works fine, > but the proceeding data is garbled. I'm using the "native" data representation for > testing, but will likely change that to something more portable when I get this > code working. > > I've included the important excerpts of the test code I'm trying to use below > (with some printf()s and error handling etc removed to make it a little more > concise). I have previously tested that std::vector allocates a contiguous flat > array of the appropriate data type in memory, so passing a pointer/reference to > the first element in such a data structure behaves the same way as simply > passing a conventional array of the appropriate data type: > > struct atom > { > int global_id; > double xyz[3]; > }; > > void write( char * fpath, std::vector<struct atom> &atoms, int rank, int nranks ) > { > /* > Memory layout information for the structure we wish to convert into > an > MPI derived data type. > */ > std::vector<int> s_blocklengths; > std::vector<MPI_Aint> s_displacements; > std::vector<MPI_Datatype> s_datatypes; > MPI_Aint addr_start, addr; > MPI_Datatype mpi_atom_type, mpi_atom_type_resized; > int type_size; > > struct atom a; > > MPI_File f; > MPI_Status stat; > MPI_Offset offset; > char *datarep = (char *)"native"; > > std::vector<int> all_N; > int local_N, global_N; > > /* > Set up the structure data type: single integer, and 3 double precision > floats. > We use the temporary "a" structure to determine the layout of memory > inside > atom structures. > */ > MPI_Get_address( &a, &addr_start ); > > s_blocklengths.push_back( 1 ); > s_datatypes.push_back( MPI_INT ); > MPI_Get_address( &a.global_id, &addr ); > s_displacements.push_back( addr - addr_start ); > > s_blocklengths.push_back( 3 ); > s_datatypes.push_back( MPI_DOUBLE ); > MPI_Get_address( &a.xyz[0], &addr ); > s_displacements.push_back( addr - addr_start ); > > MPI_Type_create_struct( (int)s_blocklengths.size(), &s_blocklengths[0], > &s_displacements[0], &s_datatypes[0], &mpi_atom_type ); > MPI_Type_commit( &mpi_atom_type ); > > /* > Take into account any compiler padding in creating an array of > structures. > */ > MPI_Type_create_resized( mpi_atom_type, 0, sizeof(struct atom), > &mpi_atom_type_resized ); > MPI_Type_commit( &mpi_atom_type_resized ); > > MPI_Type_size( mpi_atom_type_resized, &type_size ); > > local_N = (int)atoms.size(); > all_N.resize( nranks ); > > MPI_Allgather( &local_N, 1, MPI_INT, &all_N[0], 1, MPI_INT, > MPI_COMM_WORLD ); > > global_N = 0; > for( size_t i=0; i<all_N.size(); i++ ) global_N += all_N[i]; > > offset = 0; > for( int i=0; i<rank; i++ ) offset += all_N[i]; > > offset *= type_size; // convert from structure counts -> bytes into file for > true structure size > offset += sizeof( int ); // skip leading integer (global_N) in file. > > MPI_File_open( MPI_COMM_WORLD, fpath, MPI_MODE_CREATE | > MPI_MODE_WRONLY, MPI_INFO_NULL, &f ); > if( rank == 0 ) > { > MPI_File_write( f, &global_N, 1, MPI_INT, &stat ); > } > MPI_File_set_view( f, offset, mpi_atom_type_resized, > mpi_atom_type_resized, datarep, MPI_INFO_NULL ); > > MPI_File_write_all( f, &atoms[0], (int)atoms.size(), mpi_atom_type_resized, > &stat ); > MPI_File_close( &f ); > > MPI_Type_free( &mpi_atom_type ); > MPI_Type_free( &mpi_atom_type_resized ); > > return; > } > > void read( char * fpath, std::vector<struct atom> &atoms ) > { > std::vector<int> s_blocklengths; > std::vector<MPI_Aint> s_displacements; > std::vector<MPI_Datatype> s_datatypes; > MPI_Datatype mpi_atom_type, mpi_atom_type_resized; > > struct atom a; > MPI_Aint addr_start, addr; > > MPI_File f; > MPI_Status stat; > > int global_N; > char *datarep = (char *)"native"; > > int type_size; > > /* > Set up the structure data type > */ > MPI_Get_address( &a, &addr_start ); > > s_blocklengths.push_back( 1 ); > s_datatypes.push_back( MPI_INT ); > MPI_Get_address( &a.global_id, &addr ); > s_displacements.push_back( addr - addr_start ); > > s_blocklengths.push_back( 3 ); > s_datatypes.push_back( MPI_DOUBLE ); > MPI_Get_address( &a.xyz[0], &addr ); > s_displacements.push_back( addr - addr_start ); > > MPI_Type_create_struct( (int)s_blocklengths.size(), &s_blocklengths[0], > &s_displacements[0], &s_datatypes[0], &mpi_atom_type ); > MPI_Type_commit( &mpi_atom_type ); > > /* > Take into account any compiler padding in creating an array of > structures. > */ > MPI_Type_create_resized( mpi_atom_type, 0, sizeof(struct atom), > &mpi_atom_type_resized ); > MPI_Type_commit( &mpi_atom_type_resized ); > > MPI_Type_size( mpi_atom_type_resized, &type_size ); > > MPI_File_open( MPI_COMM_SELF, fpath, MPI_MODE_RDONLY, > MPI_INFO_NULL, &f ); > > MPI_File_read( f, &global_N, 1, MPI_INT, &stat ); > > atoms.clear(); > atoms.resize( global_N ); > > errcode = MPI_File_set_view( f, sizeof(int), mpi_atom_type_resized, > mpi_atom_type_resized, datarep, MPI_INFO_NULL ); > errcode = MPI_File_read( f, &atoms[0], global_N, mpi_atom_type_resized, > &stat ); > errcode = MPI_File_close( &f ); > > MPI_Type_free( &mpi_atom_type ); > MPI_Type_free( &mpi_atom_type_resized ); > > return; > } > > Calling MPI_Type_get_extent() and MPI_Type_get_true_extent() for both > mpi_atom_type and mpi_atom_type_resized returns (0,32) bytes in all cases. > Calling MPI_Type_size() on both derived data types returns 28 bytes. > > If I call MPI_File_get_type_extent() on both derived data types after opening the > file, they both resolve to 32 bytes - so I think the problem is in the difference > between the data representation in memory and on disk. If I explicitly use 32 > bytes in the offset calculation in the write() routine above, it still doesn't work. > > I'm finding it remarkably difficult to do something very simple using MPI's > derived data types and the parallel IO, and hence I'm guessing that I have > fundamentally misunderstood one or more aspects of this. If anyone can help > clarify where I'm going wrong, that would be much appreciated! > > Cheers, > > John. > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Use of MPI derived data types / MPI file IO
by jgrime＠uchicago.edu 18 Nov '12

18 Nov '12

Hi all, I'm having some problems with using derived data types and MPI parallel IO, and was wondering if anyone could help. I tried to search the archives in case this was covered earlier, but that just gave me "ht://Dig error" messages. Outline: I have written a C++ program where each MPI rank acts on data stored in a local array of structures. The arrays are typically of different lengths on each rank. I wish to write and read the contents of these arrays to disk using MPI's parallel IO routines. The file format is simply an initial integer which describes how many "structures" are in the file, followed by the data which represents the "structure information" from all ranks (ie the total data set). So far, I've tried two different approaches: the first consists of each rank serialising the contents of the local array of structures into a byte array, which is then saved to file "f" using MPI_File_set_view( f, MPI_COMM_WORLD, offset, MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL ) to skip the initial integer "header" and then a call to MPI_File_write_all( f, local_bytearray, local_n_bytes, MPI_CHAR, &status ). Here, "offset" is simply the size of an integer (in bytes) + the summation of the number of bytes each preceeding rank wishes to write to the file (received via an earlier MPI_Allgather call). This seems to work, as when I read the file back in on a single MPI rank and deserialise the data into an array of structures I get the results I expect. The second approach is to use MPI's derived data types to create MPI representations of the structures, and then treat the arrays of structures as MPI data types. This allows me to avoid copying the local data into an intermediate buffer etc, and seems the more elegant approach. I cannot, however, seem to make this approach work. I'm pretty sure the problem lies in my use of the file views, but I'm not sure where I'm going wrong. The reading of the integer "header" always works fine, but the proceeding data is garbled. I'm using the "native" data representation for testing, but will likely change that to something more portable when I get this code working. I've included the important excerpts of the test code I'm trying to use below (with some printf()s and error handling etc removed to make it a little more concise). I have previously tested that std::vector allocates a contiguous flat array of the appropriate data type in memory, so passing a pointer/reference to the first element in such a data structure behaves the same way as simply passing a conventional array of the appropriate data type: struct atom { int global_id; double xyz[3]; }; void write( char * fpath, std::vector<struct atom> &atoms, int rank, int nranks ) { /* Memory layout information for the structure we wish to convert into an MPI derived data type. */ std::vector<int> s_blocklengths; std::vector<MPI_Aint> s_displacements; std::vector<MPI_Datatype> s_datatypes; MPI_Aint addr_start, addr; MPI_Datatype mpi_atom_type, mpi_atom_type_resized; int type_size; struct atom a; MPI_File f; MPI_Status stat; MPI_Offset offset; char *datarep = (char *)"native"; std::vector<int> all_N; int local_N, global_N; /* Set up the structure data type: single integer, and 3 double precision floats. We use the temporary "a" structure to determine the layout of memory inside atom structures. */ MPI_Get_address( &a, &addr_start ); s_blocklengths.push_back( 1 ); s_datatypes.push_back( MPI_INT ); MPI_Get_address( &a.global_id, &addr ); s_displacements.push_back( addr - addr_start ); s_blocklengths.push_back( 3 ); s_datatypes.push_back( MPI_DOUBLE ); MPI_Get_address( &a.xyz[0], &addr ); s_displacements.push_back( addr - addr_start ); MPI_Type_create_struct( (int)s_blocklengths.size(), &s_blocklengths[0], &s_displacements[0], &s_datatypes[0], &mpi_atom_type ); MPI_Type_commit( &mpi_atom_type ); /* Take into account any compiler padding in creating an array of structures. */ MPI_Type_create_resized( mpi_atom_type, 0, sizeof(struct atom), &mpi_atom_type_resized ); MPI_Type_commit( &mpi_atom_type_resized ); MPI_Type_size( mpi_atom_type_resized, &type_size ); local_N = (int)atoms.size(); all_N.resize( nranks ); MPI_Allgather( &local_N, 1, MPI_INT, &all_N[0], 1, MPI_INT, MPI_COMM_WORLD ); global_N = 0; for( size_t i=0; i<all_N.size(); i++ ) global_N += all_N[i]; offset = 0; for( int i=0; i<rank; i++ ) offset += all_N[i]; offset *= type_size; // convert from structure counts -> bytes into file for true structure size offset += sizeof( int ); // skip leading integer (global_N) in file. MPI_File_open( MPI_COMM_WORLD, fpath, MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &f ); if( rank == 0 ) { MPI_File_write( f, &global_N, 1, MPI_INT, &stat ); } MPI_File_set_view( f, offset, mpi_atom_type_resized, mpi_atom_type_resized, datarep, MPI_INFO_NULL ); MPI_File_write_all( f, &atoms[0], (int)atoms.size(), mpi_atom_type_resized, &stat ); MPI_File_close( &f ); MPI_Type_free( &mpi_atom_type ); MPI_Type_free( &mpi_atom_type_resized ); return; } void read( char * fpath, std::vector<struct atom> &atoms ) { std::vector<int> s_blocklengths; std::vector<MPI_Aint> s_displacements; std::vector<MPI_Datatype> s_datatypes; MPI_Datatype mpi_atom_type, mpi_atom_type_resized; struct atom a; MPI_Aint addr_start, addr; MPI_File f; MPI_Status stat; int global_N; char *datarep = (char *)"native"; int type_size; /* Set up the structure data type */ MPI_Get_address( &a, &addr_start ); s_blocklengths.push_back( 1 ); s_datatypes.push_back( MPI_INT ); MPI_Get_address( &a.global_id, &addr ); s_displacements.push_back( addr - addr_start ); s_blocklengths.push_back( 3 ); s_datatypes.push_back( MPI_DOUBLE ); MPI_Get_address( &a.xyz[0], &addr ); s_displacements.push_back( addr - addr_start ); MPI_Type_create_struct( (int)s_blocklengths.size(), &s_blocklengths[0], &s_displacements[0], &s_datatypes[0], &mpi_atom_type ); MPI_Type_commit( &mpi_atom_type ); /* Take into account any compiler padding in creating an array of structures. */ MPI_Type_create_resized( mpi_atom_type, 0, sizeof(struct atom), &mpi_atom_type_resized ); MPI_Type_commit( &mpi_atom_type_resized ); MPI_Type_size( mpi_atom_type_resized, &type_size ); MPI_File_open( MPI_COMM_SELF, fpath, MPI_MODE_RDONLY, MPI_INFO_NULL, &f ); MPI_File_read( f, &global_N, 1, MPI_INT, &stat ); atoms.clear(); atoms.resize( global_N ); errcode = MPI_File_set_view( f, sizeof(int), mpi_atom_type_resized, mpi_atom_type_resized, datarep, MPI_INFO_NULL ); errcode = MPI_File_read( f, &atoms[0], global_N, mpi_atom_type_resized, &stat ); errcode = MPI_File_close( &f ); MPI_Type_free( &mpi_atom_type ); MPI_Type_free( &mpi_atom_type_resized ); return; } Calling MPI_Type_get_extent() and MPI_Type_get_true_extent() for both mpi_atom_type and mpi_atom_type_resized returns (0,32) bytes in all cases. Calling MPI_Type_size() on both derived data types returns 28 bytes. If I call MPI_File_get_type_extent() on both derived data types after opening the file, they both resolve to 32 bytes - so I think the problem is in the difference between the data representation in memory and on disk. If I explicitly use 32 bytes in the offset calculation in the write() routine above, it still doesn't work. I'm finding it remarkably difficult to do something very simple using MPI's derived data types and the parallel IO, and hence I'm guessing that I have fundamentally misunderstood one or more aspects of this. If anyone can help clarify where I'm going wrong, that would be much appreciated! Cheers, John.

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shell in emacs
by Hui Zhang 17 Nov '12

17 Nov '12

Hi, I M-x shell in emacs and compile, run the hell world. My shell is closed by mpi after running which I do not expect. ~> mpiexec -np 1 ./hello Process 0 on Hui-Zhangs-MacBook-Air.local out of 1 Process shell finished But when I run in a real terminal, no problem. When I use openmpi and stil run in emacs, also no problem, i.e. the shell is still alive. Thanks for any suggestions! Hui

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Re: [mpich-discuss] mpich 3.0rc1 Ubuntu, Debian and Slackware packages (x86 and amd64)
by Pavan Balaji 17 Nov '12

17 Nov '12

Updated the downloads page. Thanks. http://www.mpich.org/downloads/ On 11/14/2012 12:35 PM US Central Time, Marcelo Soares Souza wrote: > Last mpich 3.0rc1 packages, enjoy! :) > > * Ubuntu 12.04.1 LTS (Precise Pangolin) > > - amd64 > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.0rc1/mpich_3.0rc1-1ubuntu… > > - x86 > http://www.cebacad.net/files/mpich/ubuntu/mpich-3.0rc1/mpich_3.0rc1-1ubuntu… > > * Debian 7.0 (Wheezy) > > - amd64 > http://www.cebacad.net/files/mpich/debian/mpich-3.0rc1/mpich_3.0rc1-1debian… > > - x86 > http://www.cebacad.net/files/mpich/debian/mpich-3.0rc1/mpich_3.0rc1-1debian… > > * Slackware 14.0 > > - amd64 > http://www.cebacad.net/files/mpich/slackware/mpich-3.0rc1/mpich-3.0rc1-x86_… > > - x86 > http://www.cebacad.net/files/mpich/slackware/mpich-3.0rc1/mpich-3.0rc1-i486… > -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1
by Darius Buntinas 16 Nov '12

16 Nov '12

There are certain warnings that the compiler will only check with optimization enabled. To get all warnings, -O2 must be included. -d On Nov 16, 2012, at 11:52 AM, Yauheni Zelenko wrote: > Hi, Darius! > > But why warnings flags are mixed with optimization ones? I think these options should be independent. > > Eugene. > ________________________________________ > From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] On Behalf Of Darius Buntinas [buntinas(a)mcs.anl.gov] > Sent: Friday, November 16, 2012 9:41 AM > To: discuss(a)mpich.org > Cc: mpich-discuss(a)mcs.anl.gov > Subject: Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1 > > The --enable-strict flag adds -O2. Try --enable-strict=noopt. > > -d > > > On Nov 15, 2012, at 7:06 PM, Yauheni Zelenko wrote: > >> Hi! >> >> I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. >> >> For optimize configuration command like contains -O2 and -O3: >> >> ./configure --prefix=${InstallDir} \ >> --with-pm=hydra --with-device=ch3:nemesis \ >> --disable-chekpointing \ >> --enable-strict --enable-fast=O3 \ >> --disable-f77 --disable-fc \ >> CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ >> CPP=${GCCDir}/bin/cpp \ >> CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ >> CXXCPP=${GCCDir}/bin/cpp >> >> For debug one -O2, but optimization is disabled: >> >> ./configure --prefix=${InstallDir} \ >> --with-pm=hydra --with-device=ch3:nemesis \ >> --disable-chekpointing \ >> --enable-strict --disable-fast -enable-g=debug \ >> --disable-f77 --disable-fc \ >> CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ >> CPP=${GCCDir}/bin/cpp \ >> CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ >> CXXCPP=${GCCDir}/bin/cpp >> >> Eugene. >> _______________________________________________ >> 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] Compiler optimization flags in MPICH 3.0 rc1
by Pavan Balaji 16 Nov '12

16 Nov '12

On 11/16/2012 11:52 AM US Central Time, Yauheni Zelenko wrote: > But why warnings flags are mixed with optimization ones? I think > these options should be independent. They are, unfortunately, not independent. Some compilers throw some errors only when the optimization flag is specified. That's the reason why we have both options --enable-strict and --enable-strict=noopt. -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

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Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1
by Yauheni Zelenko 16 Nov '12

16 Nov '12

Hi, Darius! But why warnings flags are mixed with optimization ones? I think these options should be independent. Eugene. ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] On Behalf Of Darius Buntinas [buntinas(a)mcs.anl.gov] Sent: Friday, November 16, 2012 9:41 AM To: discuss(a)mpich.org Cc: mpich-discuss(a)mcs.anl.gov Subject: Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1 The --enable-strict flag adds -O2. Try --enable-strict=noopt. -d On Nov 15, 2012, at 7:06 PM, Yauheni Zelenko wrote: > Hi! > > I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. > > For optimize configuration command like contains -O2 and -O3: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --enable-fast=O3 \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > For debug one -O2, but optimization is disabled: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --disable-fast -enable-g=debug \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > Eugene. > _______________________________________________ > 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] MPI i/o like fopen (filename, "rb")
by Jeff Hammond 16 Nov '12

16 Nov '12

You can Google or go to http://www.mcs.anl.gov/research/projects/mpi/www/www3/ to get documentation for how to use the following commands: MPI_File_get_size MPI_File_open MPI_File_read MPI_File_write MPI_File_close These are the ones you need to do a straightforward conversion of your code. Best, Jeff On Fri, Nov 16, 2012 at 11:34 AM, Muhammad Zulfikar Handana <zulfikarhandana(a)gmail.com> wrote: > dear, > i have a little confused about MPI i/o, because iam new for this > programming. i have some question. > if i want make some program with this code > > 1) > > int get_size(char *filename) > { > struct stat buf; > stat(filename,&buf); > int j =buf.st_size; > > return j; > } > > 2) > key = fopen(key_file, "rb"); > fread(Kunci, pk, 1, key); > for(i=0;i<Nk*4;i++) > Key[i]=Kunci[i]; > > 3) hasil = fopen (file_akhir, "wb"); > for (k=0;k<(((block-1)*16)+pad);k++) > { > fputc(output[k], hasil); > } > fclose (hasil); > > how to translate that code into MPI i / o ? > thanks a lot for your attention > > Regards > > > Handana > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

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Re: [mpich-discuss] Compiler optimization flags in MPICH 3.0 rc1
by Darius Buntinas 16 Nov '12

16 Nov '12

The --enable-strict flag adds -O2. Try --enable-strict=noopt. -d On Nov 15, 2012, at 7:06 PM, Yauheni Zelenko wrote: > Hi! > > I tried to build optimize and debug version of MPICH 3.0 rc1 and noticed some problems with compiler optimization flags. Looks like -O2 is set implicitly. > > For optimize configuration command like contains -O2 and -O3: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --enable-fast=O3 \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > For debug one -O2, but optimization is disabled: > > ./configure --prefix=${InstallDir} \ > --with-pm=hydra --with-device=ch3:nemesis \ > --disable-chekpointing \ > --enable-strict --disable-fast -enable-g=debug \ > --disable-f77 --disable-fc \ > CC=${GCCDir}/bin/gcc CFLAGS="-m32 -fPIC" \ > CPP=${GCCDir}/bin/cpp \ > CXX=${GCCDir}/bin/g++ CXXFLAGS="-m32 -fPIC" \ > CXXCPP=${GCCDir}/bin/cpp > > Eugene. > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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