December 2021 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Installation error: size of array element is not a multiple of its alignment
by Douglas G Dommermuth 29 Dec '21

29 Dec '21

Dear mpich.org<http://mpich.org>, I was able to compile with gcc 10.2.0. Thank you, Doug. On Dec 29, 2021, at 9:40 AM, Douglas G Dommermuth <dgd(a)mit.edu<mailto:[email protected]>> wrote: Dear mpich.org<http://mpich.org/>, I apologize. I sent this email out with the wrong subject matter. Here is the correct subject. Thank you. I am getting an error installing mpich-3.4.3 on a MacBook Air (M1,2020) with macOS Monterey 12.1, gcc 11.2.0, g++ 11.2.0, and gfortran 11.2.0. I used the following commands: ./configure FFLAGS=-fallow-argument-mismatch --prefix=/Users/douglasdommermuth/mpich2/mpich2-install | & tee c.txt make clean make V=1 | & tee m.txt I get the following error: CC src/mpi/attr/lib_libpmpi_la-attr_delete.lo In file included from ./src/mpid/ch4/netmod/include/../ofi/ofi_impl.h:10, from ./src/mpid/ch4/netmod/include/../ofi/ofi_am.h:8, from ./src/mpid/ch4/netmod/include/../ofi/netmod_inline.h:9, from ./src/mpid/ch4/netmod/include/netmod_impl.h:1644, from ./src/mpid/ch4/include/mpidch4.h:322, from ./src/mpid/ch4/include/mpidpost.h:10, from ./src/include/mpiimpl.h:241, from src/mpi/attr/attr_delete.c:6: ./src/mpid/ch4/netmod/include/../ofi/ofi_types.h:326:5: error: size of array element is not a multiple of its alignment 326 | MPIDI_OFI_cacheline_mutex_t mutexes[MAX_OFI_MUTEXES]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [src/mpi/attr/lib_libpmpi_la-attr_delete.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 An online search indicates that others are experiencing this error with gcc 11. For example, here https://github.com/JayDDee/cpuminer-opt/issues/313, https://gitlab.com/xonotic/darkplaces/-/issues/363, and https://github.com/relic-toolkit/relic/issues/202. I have not tried an earlier version of gcc. Compressed versions of c.txt, m.txt, and config log files are attached. Thank you, Doug. <m.txt.gz><c.txt.gz><config.log.gz><src_pm_hydra_config.log.gz><src_mpl_config.log.gz>

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Installation error: size of array element is not a multiple of its alignment
by Douglas G Dommermuth 29 Dec '21

29 Dec '21

Dear mpich.org<http://mpich.org/>, I apologize. I sent this email out with the wrong subject matter. Here is the correct subject. Thank you. I am getting an error installing mpich-3.4.3 on a MacBook Air (M1,2020) with macOS Monterey 12.1, gcc 11.2.0, g++ 11.2.0, and gfortran 11.2.0. I used the following commands: ./configure FFLAGS=-fallow-argument-mismatch --prefix=/Users/douglasdommermuth/mpich2/mpich2-install | & tee c.txt make clean make V=1 | & tee m.txt I get the following error: CC src/mpi/attr/lib_libpmpi_la-attr_delete.lo In file included from ./src/mpid/ch4/netmod/include/../ofi/ofi_impl.h:10, from ./src/mpid/ch4/netmod/include/../ofi/ofi_am.h:8, from ./src/mpid/ch4/netmod/include/../ofi/netmod_inline.h:9, from ./src/mpid/ch4/netmod/include/netmod_impl.h:1644, from ./src/mpid/ch4/include/mpidch4.h:322, from ./src/mpid/ch4/include/mpidpost.h:10, from ./src/include/mpiimpl.h:241, from src/mpi/attr/attr_delete.c:6: ./src/mpid/ch4/netmod/include/../ofi/ofi_types.h:326:5: error: size of array element is not a multiple of its alignment 326 | MPIDI_OFI_cacheline_mutex_t mutexes[MAX_OFI_MUTEXES]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [src/mpi/attr/lib_libpmpi_la-attr_delete.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 An online search indicates that others are experiencing this error with gcc 11. For example, here https://github.com/JayDDee/cpuminer-opt/issues/313, https://gitlab.com/xonotic/darkplaces/-/issues/363, and https://github.com/relic-toolkit/relic/issues/202. I have not tried an earlier version of gcc. Compressed versions of c.txt, m.txt, and config log files are attached. Thank you, Doug.

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Re: [mpich-discuss] Optimizing runtime for 4 mpiexec.hydra jobs
by Douglas G Dommermuth 29 Dec '21

29 Dec '21

Dear mpich.org<http://mpich.org>, I am getting an error installing mpich-3.4.3 on a MacBook Air (M1,2020) with macOS Monterey 12.1, gcc 11.2.0, g++ 11.2.0, and gfortran 11.2.0. I used the following commands: ./configure FFLAGS=-fallow-argument-mismatch --prefix=/Users/douglasdommermuth/mpich2/mpich2-install | & tee c.txt make clean make V=1 | & tee m.txt I get the following error: CC src/mpi/attr/lib_libpmpi_la-attr_delete.lo In file included from ./src/mpid/ch4/netmod/include/../ofi/ofi_impl.h:10, from ./src/mpid/ch4/netmod/include/../ofi/ofi_am.h:8, from ./src/mpid/ch4/netmod/include/../ofi/netmod_inline.h:9, from ./src/mpid/ch4/netmod/include/netmod_impl.h:1644, from ./src/mpid/ch4/include/mpidch4.h:322, from ./src/mpid/ch4/include/mpidpost.h:10, from ./src/include/mpiimpl.h:241, from src/mpi/attr/attr_delete.c:6: ./src/mpid/ch4/netmod/include/../ofi/ofi_types.h:326:5: error: size of array element is not a multiple of its alignment 326 | MPIDI_OFI_cacheline_mutex_t mutexes[MAX_OFI_MUTEXES]; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: *** [src/mpi/attr/lib_libpmpi_la-attr_delete.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 An online search indicates that others are experiencing this error with gcc 11. For example, here https://github.com/JayDDee/cpuminer-opt/issues/313, https://gitlab.com/xonotic/darkplaces/-/issues/363, and https://github.com/relic-toolkit/relic/issues/202. I have not tried an earlier version of gcc. Compressed versions of c.txt, m.txt, and config log files are attached. Thank you, Doug.

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Re: [mpich-discuss] [EXTERNAL] Re: Issue with MPICH 4.0b1 and MPI I/O and ROMIO...maybe?
by Zhou, Hui 23 Dec '21

23 Dec '21

> Also, I don't see --with-file-system in the configure help? Does > the MPICH configure "pass down" the option to (I assume) > ROMIO? Just to confirm that MPICH configure will pass down all options including that MPICH itself is not aware. We probably should make MPICH "aware" of these options to provide better user helps. -- Hui Zhou

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Re: [mpich-discuss] [EXTERNAL] Re: Issue with MPICH 4.0b1 and MPI I/O and ROMIO...maybe?
by Latham, Robert J. 22 Dec '21

22 Dec '21

On Wed, 2021-12-22 at 17:35 +0000, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] wrote: > Rob, > > Thanks. So for a cluster that is mainly "regular linux" (not sure > what they run for non-GPFS), GPFS, some tmpfs probably, and a whole > bunch of NFS, what would recommend as a good set of filesystems? > Would something like: > > --with-file-system=gpfs > > be enough, or once you have that flag does that do enough? If you have any gpfs anywhere, then yeah, you can add the 'gpfs' flag. You probably want "--with-file-system=ufs+gpfs" ROMIO has an NFS driver but I'll warn you it is not -- and in fact cannot be -- very good. There are many cases where if you try to write data to NFS in paralllel you will end up with corrupted data. If you do manage to not get data corruption, your performance will be terrible because ROMIO tried really really hard to ensure data correctness (wrapping each and every I/O call with a lock/unlock in an effort to force client-side data cache flushes). > Also, I don't see --with-file-system in the configure help? Does the > MPICH configure "pass down" the option to (I assume) ROMIO? correct. ROMIO is both it's own thing and part of MPICH. Uh, sorry about that. ==rob > Matt > -- > Matt Thompson, SSAI, Ld Scientific Programmer/Analyst > NASA GSFC, Global Modeling and Assimilation Office > Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 > Phone: 301-614-6712 Fax: 301-614-6246 > http://science.gsfc.nasa.gov/sed/bio/matthew.thompson > > On 12/20/21, 10:21 AM, "Latham, Robert J." <robl(a)mcs.anl.gov> wrote: > > On Fri, 2021-12-17 at 19:10 +0000, Thompson, Matt (GSFC- > 610.1)[SCIENCE > SYSTEMS AND APPLICATIONS INC] via discuss wrote: > > MPICH Discuss, > NetCDF: Error initializing for parallel access > > > > I did a bit of debugging and found that the crash was due to an > > environment variable that was set because my application > mistakenly > > thought I was running Intel MPI (mainly because we didn't have > > detection for MPICH, so it defaulted to our "default" on this > cluster > > of Intel MPI). When it sees Intel MPI, it sets: > > > > ROMIO_FSTYPE_FORCE="gpfs:" > > > > which we've found is useful when running with Intel MPI on our > GPFS > > system. > > Hah I had no idea anyone besides me was using this little > feature. Here's a bit more information for context: > > > https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpress3.mc… > > > > So, of course the "right" thing to do is not to set that. > (Doctor, it > > hurts when I do this. So stop doing that.) > > > > But it got me wondering, is there perhaps a "better" way I > should be > > building MPICH? Should this flag cause this sort of crash? Or > does it > > mean I build MPICH/ROMIO incorrectly or incompletely (no GPFS > > support, say)? > > Intel MPI has its own way of supporting extra file systems, via > the "I_MPI_EXTRA_FILESYSTEM" environment variable. > > > https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpress3.mc… > > I'm open to suggestions on how ROMIO should best handle this > situation. You requested a file system (gpfs) that ROMIO did not > support. ROMIO could fall back to "generic unix file system" but you > asked explicitly for GPFS, presumably for a good reason (or in your > case, by accident but ROMIO is not a mind reader...) > > If you are building your own MPICH, add the `--with-file- > system=...` flag. that is a '+'-delmited list of file systems. for > example: > > `--with-file-system=ufs+testfs+gpfs+lustre+panfs+pvfs2+unify` > > I try to build everything I can so my list is quite long. Yours > will be shorter -- if you pick a file system for which you do not > have development headers and libraries, your build will fail > (hopefully at configure time). > > ==rob >

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Re: [mpich-discuss] [EXTERNAL] Re: Issue with MPICH 4.0b1 and MPI I/O and ROMIO...maybe?
by Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] 22 Dec '21

22 Dec '21

Rob, Thanks. So for a cluster that is mainly "regular linux" (not sure what they run for non-GPFS), GPFS, some tmpfs probably, and a whole bunch of NFS, what would recommend as a good set of filesystems? Would something like: --with-file-system=gpfs be enough, or once you have that flag does that do enough? Also, I don't see --with-file-system in the configure help? Does the MPICH configure "pass down" the option to (I assume) ROMIO? Matt -- Matt Thompson, SSAI, Ld Scientific Programmer/Analyst NASA GSFC, Global Modeling and Assimilation Office Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 Phone: 301-614-6712 Fax: 301-614-6246 http://science.gsfc.nasa.gov/sed/bio/matthew.thompson On 12/20/21, 10:21 AM, "Latham, Robert J." <robl(a)mcs.anl.gov> wrote: On Fri, 2021-12-17 at 19:10 +0000, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] via discuss wrote: > MPICH Discuss, NetCDF: Error initializing for parallel access > > I did a bit of debugging and found that the crash was due to an > environment variable that was set because my application mistakenly > thought I was running Intel MPI (mainly because we didn't have > detection for MPICH, so it defaulted to our "default" on this cluster > of Intel MPI). When it sees Intel MPI, it sets: > > ROMIO_FSTYPE_FORCE="gpfs:" > > which we've found is useful when running with Intel MPI on our GPFS > system. Hah I had no idea anyone besides me was using this little feature. Here's a bit more information for context: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpress3.mc… > So, of course the "right" thing to do is not to set that. (Doctor, it > hurts when I do this. So stop doing that.) > > But it got me wondering, is there perhaps a "better" way I should be > building MPICH? Should this flag cause this sort of crash? Or does it > mean I build MPICH/ROMIO incorrectly or incompletely (no GPFS > support, say)? Intel MPI has its own way of supporting extra file systems, via the "I_MPI_EXTRA_FILESYSTEM" environment variable. https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpress3.mc… I'm open to suggestions on how ROMIO should best handle this situation. You requested a file system (gpfs) that ROMIO did not support. ROMIO could fall back to "generic unix file system" but you asked explicitly for GPFS, presumably for a good reason (or in your case, by accident but ROMIO is not a mind reader...) If you are building your own MPICH, add the `--with-file-system=...` flag. that is a '+'-delmited list of file systems. for example: `--with-file-system=ufs+testfs+gpfs+lustre+panfs+pvfs2+unify` I try to build everything I can so my list is quite long. Yours will be shorter -- if you pick a file system for which you do not have development headers and libraries, your build will fail (hopefully at configure time). ==rob

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Re: [mpich-discuss] Issue with MPICH 4.0b1 and MPI I/O and ROMIO...maybe?
by Latham, Robert J. 20 Dec '21

20 Dec '21

On Fri, 2021-12-17 at 19:10 +0000, Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] via discuss wrote: > MPICH Discuss, NetCDF: Error initializing for parallel access > > I did a bit of debugging and found that the crash was due to an > environment variable that was set because my application mistakenly > thought I was running Intel MPI (mainly because we didn't have > detection for MPICH, so it defaulted to our "default" on this cluster > of Intel MPI). When it sees Intel MPI, it sets: > > ROMIO_FSTYPE_FORCE="gpfs:" > > which we've found is useful when running with Intel MPI on our GPFS > system. Hah I had no idea anyone besides me was using this little feature. Here's a bit more information for context: https://press3.mcs.anl.gov/romio/2019/02/20/useful-environment-variables/ > So, of course the "right" thing to do is not to set that. (Doctor, it > hurts when I do this. So stop doing that.) > > But it got me wondering, is there perhaps a "better" way I should be > building MPICH? Should this flag cause this sort of crash? Or does it > mean I build MPICH/ROMIO incorrectly or incompletely (no GPFS > support, say)? Intel MPI has its own way of supporting extra file systems, via the "I_MPI_EXTRA_FILESYSTEM" environment variable. https://press3.mcs.anl.gov/romio/2014/06/12/romio-and-intel-mpi/ I'm open to suggestions on how ROMIO should best handle this situation. You requested a file system (gpfs) that ROMIO did not support. ROMIO could fall back to "generic unix file system" but you asked explicitly for GPFS, presumably for a good reason (or in your case, by accident but ROMIO is not a mind reader...) If you are building your own MPICH, add the `--with-file-system=...` flag. that is a '+'-delmited list of file systems. for example: `--with-file-system=ufs+testfs+gpfs+lustre+panfs+pvfs2+unify` I try to build everything I can so my list is quite long. Yours will be shorter -- if you pick a file system for which you do not have development headers and libraries, your build will fail (hopefully at configure time). ==rob

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Issue with MPICH 4.0b1 and MPI I/O and ROMIO...maybe?
by Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] 17 Dec '21

17 Dec '21

MPICH Discuss, So this is an odd one. Thanks to Hui Zhou from this list, I was able to build MPICH 4.0b1. I proceeded to build libraries and my application that I work on. And all seemed to compile just well. I then ran my model and...crash: Error opening file species.data -115 NetCDF: Error initializing for parallel access I did a bit of debugging and found that the crash was due to an environment variable that was set because my application mistakenly thought I was running Intel MPI (mainly because we didn't have detection for MPICH, so it defaulted to our "default" on this cluster of Intel MPI). When it sees Intel MPI, it sets: ROMIO_FSTYPE_FORCE="gpfs:" which we've found is useful when running with Intel MPI on our GPFS system. I whipped up a little netCDF reader executable that essentially does: call check( nf90_open(FILE_NAME, IOR(NF90_NOWRITE, NF90_MPIIO), comm=MPI_COMM_WORLD, info=MPI_INFO_NULL, ncid=ncid) ) and then: $ mpirun -np 2 ./simple_xy_rd_mpiio.exe OX_in(1,1:5): 7.1448361893544643E-008 1.7177123368128377E-007 2.8831971121690003E-007 3.7688394627366506E-007 4.6076729631749913E-007 OX_in(1,1:5): 7.1448361893544643E-008 1.7177123368128377E-007 2.8831971121690003E-007 3.7688394627366506E-007 4.6076729631749913E-007 *** SUCCESS reading example file species.data! *** SUCCESS reading example file species.data! $ ROMIO_FSTYPE_FORCE="gpfs:" mpirun -np 2 ./simple_xy_rd_mpiio.exe NetCDF: Error initializing for parallel access NetCDF: Error initializing for parallel access STOP Stopped STOP Stopped So, of course the "right" thing to do is not to set that. (Doctor, it hurts when I do this. So stop doing that.) But it got me wondering, is there perhaps a "better" way I should be building MPICH? Should this flag cause this sort of crash? Or does it mean I build MPICH/ROMIO incorrectly or incompletely (no GPFS support, say)? Thanks, Matt -- Matt Thompson, SSAI, Ld Scientific Programmer/Analyst NASA GSFC, Global Modeling and Assimilation Office Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 Phone: 301-614-6712 Fax: 301-614-6246 http://science.gsfc.nasa.gov/sed/bio/matthew.thompson

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Re: [mpich-discuss] [EXTERNAL] Re: Help Building MPICH 4.0b1: undefined references to hwloc
by Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] 17 Dec '21

17 Dec '21

Hui, Sorry for the late reply, but yep, that worked! I have MPICH! And it did helloworld. Now for complex things (aka hoping that ESMF's "mpich3" settings work with MPICH4!). Matt -- Matt Thompson, SSAI, Ld Scientific Programmer/Analyst NASA GSFC, Global Modeling and Assimilation Office Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 Phone: 301-614-6712 Fax: 301-614-6246 http://science.gsfc.nasa.gov/sed/bio/matthew.thompson From: "Zhou, Hui" <zhouh(a)anl.gov> Date: Wednesday, December 15, 2021 at 10:44 AM To: "Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC]" <matthew.thompson(a)nasa.gov>, "discuss(a)mpich.org" <discuss(a)mpich.org> Subject: Re: [EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc Hi Matt, Thanks for posting config.log. I found the issue. Both mpich the library and hydra the program uses hwloc and independently tries to probe hwloc. Because hydra is configured as a subdir inside mpich configure, it inherits the CFLAGS from mpich, resulting in using embedded hwloc.h while linking with external libhwloc. We'll patch mpich to strengthen its config check. Meanwhile, you can pass --with-hwloc=embedded to the mpich configure to force both mpich and hydra to use embedded hwloc, which should bypass your issue. Thanks for reporting! -- Hui Zhou ________________________________ From: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson(a)nasa.gov> Sent: Wednesday, December 15, 2021 7:13 AM To: discuss(a)mpich.org <discuss(a)mpich.org> Cc: Zhou, Hui <zhouh(a)anl.gov> Subject: Re: [EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc Hui, Please find attached the requested config.log Matt -- Matt Thompson, SSAI, Ld Scientific Programmer/Analyst NASA GSFC, Global Modeling and Assimilation Office Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 Phone: 301-614-6712 Fax: 301-614-6246 http://science.gsfc.nasa.gov/sed/bio/matthew.thompson From: "Zhou, Hui via discuss" <discuss(a)mpich.org> Reply-To: "discuss(a)mpich.org" <discuss(a)mpich.org> Date: Tuesday, December 14, 2021 at 6:14 PM To: "discuss(a)mpich.org" <discuss(a)mpich.org> Cc: "Zhou, Hui" <zhouh(a)anl.gov> Subject: [EXTERNAL] Re: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc Hi Matt, Could post your src/pm/hydra/config.log? -- Hui Zhou ________________________________ From: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] via discuss <discuss(a)mpich.org> Sent: Tuesday, December 14, 2021 2:40 PM To: discuss(a)mpich.org <discuss(a)mpich.org> Cc: Thompson, Matt (GSFC-610.1)[SCIENCE SYSTEMS AND APPLICATIONS INC] <matthew.thompson(a)nasa.gov> Subject: [mpich-discuss] Help Building MPICH 4.0b1: undefined references to hwloc MPICH Discuss, I'm sure I've done something stupid, but I'm not sure what. I tried searching google, but my google-fu failed me. Today I decided to try and build MPICH 4.0b1 on a cluster I'm on (NCCS Discover) using GCC 11.2. My configure line was quite boring: ./configure CC=gcc CXX=g++ FC=gfortran \ FCFLAGS=-fallow-argument-mismatch \ FFLAGS=-fallow-argument-mismatch \ --prefix=/discover/swdev/gmao_SIteam/MPI/mpich/4.0b1/gcc-11.2.0 The MPICH configure step was nice enough to let me know I needed those FFLAGS and FCFLAGS. And it configured just happily.[1] When I went to the make step I eventually it errored out with: make[3]: Entering directory '/gpfsm/dswdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra' CCLD libpm.la CCLD hydra_persist /usr/bin/ld: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra/.libs/libhydra.a(topo_hwloc.o): in function `HYDT_topo_hwloc_init': /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/src/pm/hydra/tools/topo/hwloc/topo_hwloc.c:577: undefined reference to `hwloc_topology_set_io_types_filter' collect2: error: ld returned 1 exit status Makefile:1286: recipe for target 'hydra_persist' failed make[3]: *** [hydra_persist] Error 1 Now, as far as I can tell from the configure output, I'm using the embedded hwloc: checking if hwloc meets minimum version requirement... no configure: ===== configuring modules/hwloc ===== ... ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/modules/hwloc configure: hwloc srcdir: /discover/swdev/gmao_SIteam/MPI/src/mpich-4.0b1/modules/hwloc ... And I can't see anything in the output that it's somehow picking up on an hwloc I might have installed somewhere else (be it Open MPI or just hwloc by hand). Maybe there are flags I need to pass? I do see reference to --with-hwloc=embedded, but it looks like configure decided to use that itself. Thanks for any help, Matt [1] Note: I'm building on an Infiniband system so maybe I need to do a build with --with-device=ch4:ucx eventually, but that's a runtime thing. I figure it can't be involved with this error...right? -- Matt Thompson, SSAI, Ld Scientific Programmer/Analyst NASA GSFC, Global Modeling and Assimilation Office Code 610.1, 8800 Greenbelt Rd, Greenbelt, MD 20771 Phone: 301-614-6712 Fax: 301-614-6246 http://science.gsfc.nasa.gov/sed/bio/matthew.thompson

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Re: [mpich-discuss] make testing fails when building from git(main)
by Zhou, Hui 16 Dec '21

16 Dec '21

Could you try with the latest git repo? We just merged this PR https://github.com/pmodels/mpich/pull/5722 to fix this issue. FYI, we have changed the way we configure test suite. In the main branch, test suite, i.e. test/mpi, is now configured independently from the mpich configure. To run test suite, after build and installing mpich, go to test/mpi, run ./autogen.sh ./configure make testing We added rule in the mpich Makefile so make testing will do above as a convenience. But if you encounter issues or need customized test configuration, try configure test/mpi separately. -- Hui Zhou [https://opengraph.githubassets.com/30d95a98b05bdcdc5c065f2271e7272120785210…]<https://github.com/pmodels/mpich/pull/5722> test/config: minor fixes by raffenet · Pull Request #5722 · pmodels/mpich<https://github.com/pmodels/mpich/pull/5722> Pull Request Description Improve configure output Fix dtpools build issue Author Checklist Provide Description Particularly focus on why, not what. Reference background, issues, test failures, ... github.com ________________________________ From: Gregor Corbin via discuss <discuss(a)mpich.org> Sent: Thursday, December 16, 2021 11:48 AM To: discuss(a)mpich.org <discuss(a)mpich.org> Cc: Gregor Corbin <g.corbin(a)fz-juelich.de> Subject: [mpich-discuss] make testing fails when building from git(main) Dear MPICH devs, I want to use the MPI test suite provided with MPICH to test an MPI wrapper library I am developing (the MPI wrapper for Score-P). As a first step, I tried to check out the latest version from git, build everything and then run the test suite with `make testing`. I can build MPICH itself without a problem and the example cpi program runs just fine. However, during `make testing` I run into lots of errors of the form In file included from dtpools.c:6: ../include/dtpools_internal.h:12:10: fatal error: mpi.h: No such file or directory 12 | #include "mpi.h" | ^~~~~~~ compilation terminated. This happens only with the git version, not with the tarball version(mpich-4.0b1). I attached all the program outputs and log files. Any help is appreciated. As I workaround I first built MPICH itself, then did './configure CC=mpicc ...', in the test/mpi directory and then directly use the runtests script. This works for now, but is surely not how it was intended. Kind regards, Gregor Corbin

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