November 2017 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] mpich-3.2.1 configure with orangefs-2.9
by Jeff Hammond 14 Nov '17

14 Nov '17

The PVFS library needs to be in LD_LIBRARY_PATH or otherwise visible to the linker. Jeff On Tue, Nov 14, 2017 at 7:00 PM Weihao Liang <lwhvinson1990(a)gmail.com> wrote: > Thanks, I have sucessfully built MPICH with configure command line > "CFLAGS+='/opt/orangefs/include' ./configure --enable-romio > --with-file-system=pvfs2". But when I link the the .o file with mpicc there > are many errors as below: > ============================= > /usr/local/lib/libmpi.so: undefined reference to `PVFS_FLOAT' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_indexed' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_CHAR' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_hvector' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_resized' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_finalize' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_dist_setparam' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_perror' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_UNSIGNED_CHAR' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_wait' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_truncate' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_free' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_flush' > /usr/local/lib/libmpi.so: undefined reference to > `PVFS_debug_eventlog_to_mask' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_LONG' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_lookup' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_DOUBLE' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_SHORT' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_create' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_remove' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_BYTE' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_util_resolve' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_dist_lookup' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_io' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_vector' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_INT' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_contiguous' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_testsome' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_LONG_DOUBLE' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_struct' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_util_init_defaults' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_hindexed' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_UNSIGNED_LONG' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_isys_io' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_UNSIGNED' > /usr/local/lib/libmpi.so: undefined reference to > `PVFS_util_gen_credential_defaults' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_getparent' > /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_getattr' > collect2: error: ld returned 1 exit status > =============================================== > > Vinson > > On Tue, Nov 14, 2017 at 6:08 PM, Latham, Robert J. <robl(a)mcs.anl.gov> > wrote: > >> On Tue, 2017-11-14 at 16:54 -0600, Weihao Liang wrote: >> > Hi, all >> > >> > I have a question is that how to configure mpich-3.2.1 with orangefs- >> > 2.9 (pvfs2)? I just want to enable the MPI-IO ability when running >> > MPI program on pvfs2 filesystem. >> >> The process is still the same it has always been. OrangeFS is a >> rebranding of what we used to call PVFS v2 : >> >> Configure MPICH with the `--with-file-system=pvfs2` flag. >> >> If you want to configure other file systems, add them with '+': >> >> `configure --prefix=/usr/local/whatever --with-file-system=pvfs2+ufs` >> >> ==rob >> _______________________________________________ >> 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 -- Jeff Hammond jeff.science(a)gmail.com http://jeffhammond.github.io/ _______________________________________________ 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] mpich-3.2.1 configure with orangefs-2.9
by Weihao Liang 14 Nov '17

14 Nov '17

Thanks, I have sucessfully built MPICH with configure command line "CFLAGS+='/opt/orangefs/include' ./configure --enable-romio --with-file-system=pvfs2". But when I link the the .o file with mpicc there are many errors as below: ============================= /usr/local/lib/libmpi.so: undefined reference to `PVFS_FLOAT' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_indexed' /usr/local/lib/libmpi.so: undefined reference to `PVFS_CHAR' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_hvector' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_resized' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_finalize' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_dist_setparam' /usr/local/lib/libmpi.so: undefined reference to `PVFS_perror' /usr/local/lib/libmpi.so: undefined reference to `PVFS_UNSIGNED_CHAR' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_wait' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_truncate' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_free' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_flush' /usr/local/lib/libmpi.so: undefined reference to `PVFS_debug_eventlog_to_mask' /usr/local/lib/libmpi.so: undefined reference to `PVFS_LONG' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_lookup' /usr/local/lib/libmpi.so: undefined reference to `PVFS_DOUBLE' /usr/local/lib/libmpi.so: undefined reference to `PVFS_SHORT' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_create' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_remove' /usr/local/lib/libmpi.so: undefined reference to `PVFS_BYTE' /usr/local/lib/libmpi.so: undefined reference to `PVFS_util_resolve' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_dist_lookup' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_io' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_vector' /usr/local/lib/libmpi.so: undefined reference to `PVFS_INT' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_contiguous' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_testsome' /usr/local/lib/libmpi.so: undefined reference to `PVFS_LONG_DOUBLE' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_struct' /usr/local/lib/libmpi.so: undefined reference to `PVFS_util_init_defaults' /usr/local/lib/libmpi.so: undefined reference to `PVFS_Request_hindexed' /usr/local/lib/libmpi.so: undefined reference to `PVFS_UNSIGNED_LONG' /usr/local/lib/libmpi.so: undefined reference to `PVFS_isys_io' /usr/local/lib/libmpi.so: undefined reference to `PVFS_UNSIGNED' /usr/local/lib/libmpi.so: undefined reference to `PVFS_util_gen_credential_defaults' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_getparent' /usr/local/lib/libmpi.so: undefined reference to `PVFS_sys_getattr' collect2: error: ld returned 1 exit status =============================================== Vinson On Tue, Nov 14, 2017 at 6:08 PM, Latham, Robert J. <robl(a)mcs.anl.gov> wrote: > On Tue, 2017-11-14 at 16:54 -0600, Weihao Liang wrote: > > Hi, all > > > > I have a question is that how to configure mpich-3.2.1 with orangefs- > > 2.9 (pvfs2)? I just want to enable the MPI-IO ability when running > > MPI program on pvfs2 filesystem. > > The process is still the same it has always been. OrangeFS is a > rebranding of what we used to call PVFS v2 : > > Configure MPICH with the `--with-file-system=pvfs2` flag. > > If you want to configure other file systems, add them with '+': > > `configure --prefix=/usr/local/whatever --with-file-system=pvfs2+ufs` > > ==rob > _______________________________________________ > 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] mpich-3.2.1 configure with orangefs-2.9
by Latham, Robert J. 14 Nov '17

14 Nov '17

On Tue, 2017-11-14 at 16:54 -0600, Weihao Liang wrote: > Hi, all > > I have a question is that how to configure mpich-3.2.1 with orangefs- > 2.9 (pvfs2)? I just want to enable the MPI-IO ability when running > MPI program on pvfs2 filesystem. The process is still the same it has always been. OrangeFS is a rebranding of what we used to call PVFS v2 : Configure MPICH with the `--with-file-system=pvfs2` flag. If you want to configure other file systems, add them with '+': `configure --prefix=/usr/local/whatever --with-file-system=pvfs2+ufs` ==rob _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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mpich-3.2.1 configure with orangefs-2.9
by Weihao Liang 14 Nov '17

14 Nov '17

Hi, all I have a question is that how to configure mpich-3.2.1 with orangefs-2.9 (pvfs2)? I just want to enable the MPI-IO ability when running MPI program on pvfs2 filesystem. Thanks! _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Announcing Casper 1.0b2 release
by Min Si 14 Nov '17

14 Nov '17

We are pleased to announce the second beta release of Casper (version 1.0b2), a portable process-based asynchronous progress model for MPI communication. It contains several new features and bug fixes over the previous release. http://www.mcs.anl.gov/project/casper/downloads/ A list of changes: - Offloading-based asynchronous progress for MPI non-blocking two-sided (point-to-point) communication. - Performance profiling summary. - Hwloc based locality optimization. - Set CSP_NG=0 to fully disable Casper wrapping routines. - BUG FIX: Support error handler for COMM_SELF, inter-communicator. - BUG FIX: Fixed incompatible code with OpenMPI. Details of each change can be found in CHANGES (https://github.com/pmodels/casper/blob/master/CHANGES) Regards, The Casper Team _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Announcing the availability of mpich-3.2.1
by Kenneth Raffenetti 11 Nov '17

11 Nov '17

The MPICH team is pleased to announce the availability of a new stable release (mpich-3.2.1). This is the second stable release in the 3.2 series. It contains several bug fixes and enhancements over the previous release. All production environments are encouraged to upgrade to this release. http://www.mpich.org A list of changes in this release is included at the end of this email. Regards, The MPICH Team =============================================================================== Changes in 3.2.1 =============================================================================== # Fixes for platforms with strict memory alignment requirements. # Fixes for MPI_Win info management. # Fixed a progress bug with MPI generalized requests. # Fixed multiple integer overflow bugs in CH3 and ROMIO. # Improved detection for Fortran 2008 binding support. # Enhanced support for libfabric (OFI) netmod. # Several other minor bug fixes, memory leak fixes, and code cleanup. A full list of changes is available at the following link: http://git.mpich.org/mpich.git/shortlog/v3.2..v3.2.1 _______________________________________________ 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] FATAL MPI ERROR
by Bland, Wesley 09 Nov '17

09 Nov '17

It's very hard to tell since I don't know Chombo well, but I'd imagine that there's something wrong with the way you're configuring that. On Nov 9, 2017, at 5:22 AM, IBRAHIM NASUH YILDIRAN <iyildiran17(a)ku.edu.tr<mailto:[email protected]>> wrote: Thank you so much Wesley. However for now, I just interfere with the make file of the library. After building the library, I got the error while I was running the test cases. Hence, do I need to add or remove some flags in the make file related with the MPI? It may not be clear with this much of information but at least I want to find where I should focus on. Kind Regards, Ibrahim Nasuh YILDIRAN On Wed, Nov 8, 2017 at 10:06 PM, Bland, Wesley <wesley.bland(a)intel.com<mailto:[email protected]>> wrote: This looks like a bug in your code. MPI_ERR_ARG usually means you passed some argument into an MPI function that shouldn't be there. > On Nov 8, 2017, at 12:54 PM, IBRAHIM NASUH YILDIRAN <iyildiran17(a)ku.edu.tr<mailto:[email protected]>> wrote: > > Dear all, > > I am facing with a fatal MPI error while I am building an Adaptive Mesh Refinement library, which is Chombo, to my personal computer. The error message is "MPI_ERR_ARG: invalid argument of some other kind". The error output is also attached. I couldn't figure out what causes this error and how to solve it. I am using Ubuntu 16.04 operating system and MPICH 3.2 together with HDF5 1.10.1. > > I am very much appreciated with your help. > > Kind Regards, > Ibrahim Nasuh YILDIRAN > <Chombo-MPIError.png>_______________________________________________ > 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 _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] FATAL MPI ERROR
by IBRAHIM NASUH YILDIRAN 09 Nov '17

09 Nov '17

Thank you so much Wesley. However for now, I just interfere with the make file of the library. After building the library, I got the error while I was running the test cases. Hence, do I need to add or remove some flags in the make file related with the MPI? It may not be clear with this much of information but at least I want to find where I should focus on. Kind Regards, Ibrahim Nasuh YILDIRAN On Wed, Nov 8, 2017 at 10:06 PM, Bland, Wesley <wesley.bland(a)intel.com> wrote: > This looks like a bug in your code. MPI_ERR_ARG usually means you passed > some argument into an MPI function that shouldn't be there. > > > On Nov 8, 2017, at 12:54 PM, IBRAHIM NASUH YILDIRAN < > iyildiran17(a)ku.edu.tr> wrote: > > > > Dear all, > > > > I am facing with a fatal MPI error while I am building an Adaptive Mesh > Refinement library, which is Chombo, to my personal computer. The error > message is "MPI_ERR_ARG: invalid argument of some other kind". The error > output is also attached. I couldn't figure out what causes this error and > how to solve it. I am using Ubuntu 16.04 operating system and MPICH 3.2 > together with HDF5 1.10.1. > > > > I am very much appreciated with your help. > > > > Kind Regards, > > Ibrahim Nasuh YILDIRAN > > <Chombo-MPIError.png>_______________________________________________ > > 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] FATAL MPI ERROR
by Bland, Wesley 08 Nov '17

08 Nov '17

This looks like a bug in your code. MPI_ERR_ARG usually means you passed some argument into an MPI function that shouldn't be there. > On Nov 8, 2017, at 12:54 PM, IBRAHIM NASUH YILDIRAN <iyildiran17(a)ku.edu.tr> wrote: > > Dear all, > > I am facing with a fatal MPI error while I am building an Adaptive Mesh Refinement library, which is Chombo, to my personal computer. The error message is "MPI_ERR_ARG: invalid argument of some other kind". The error output is also attached. I couldn't figure out what causes this error and how to solve it. I am using Ubuntu 16.04 operating system and MPICH 3.2 together with HDF5 1.10.1. > > I am very much appreciated with your help. > > Kind Regards, > Ibrahim Nasuh YILDIRAN > <Chombo-MPIError.png>_______________________________________________ > 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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FATAL MPI ERROR
by IBRAHIM NASUH YILDIRAN 08 Nov '17

08 Nov '17

Dear all, I am facing with a fatal MPI error while I am building an Adaptive Mesh Refinement library, which is Chombo, to my personal computer. The error message is "MPI_ERR_ARG: invalid argument of some other kind". The error output is also attached. I couldn't figure out what causes this error and how to solve it. I am using Ubuntu 16.04 operating system and MPICH 3.2 together with HDF5 1.10.1. I am very much appreciated with your help. Kind Regards, Ibrahim Nasuh YILDIRAN _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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