The admin that rolled the hcoll rpm that we're using (and got it in
system space) said that she got it from
hpcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64.tar.
Thanks,
David
On 08/12/2015 10:51 AM, Deva wrote:
From where did you grab this HCOLL lib? MOFED or HPCX? what version?
On Wed, Aug 12, 2015 at 9:47 AM, David Shrader <dshra...@lanl.gov
<mailto:dshra...@lanl.gov>> wrote:
Hey Devendar,
It looks like I still get the error:
[dshrader@zo-fe1 tests]$ mpirun -n 2 -mca coll ^ml ./a.out
App launch reported: 1 (out of 1) daemons - 2 (out of 2) procs
[1439397957.351764] [zo-fe1:14678:0] shm.c:65 MXM WARN
Could not open the KNEM device file at /dev/knem : No such file
or direc
tory. Won't use knem.
[1439397957.352704] [zo-fe1:14677:0] shm.c:65 MXM WARN
Could not open the KNEM device file at /dev/knem : No such file
or direc
tory. Won't use knem.
[zo-fe1:14677:0] Caught signal 11 (Segmentation fault)
[zo-fe1:14678:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
2 0x0000000000056cdc mxm_handle_error()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_root/src/h
pcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:641
3 0x0000000000056e4c mxm_error_signal_handler()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_ro
ot/src/hpcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:616
4 0x00000000000326a0 killpg() ??:0
5 0x00000000000b82cb base_bcol_basesmuma_setup_library_buffers()
??:0
6 0x00000000000969e3 hmca_bcol_basesmuma_comm_query() ??:0
7 0x0000000000032ee3 hmca_coll_ml_tree_hierarchy_discovery()
coll_ml_module.c:0
8 0x000000000002fda2 hmca_coll_ml_comm_query() ??:0
9 0x000000000006ace9 hcoll_create_context() ??:0
10 0x00000000000f9706 mca_coll_hcoll_comm_query() ??:0
11 0x00000000000f684e mca_coll_base_comm_select() ??:0
12 0x0000000000073fc4 ompi_mpi_init() ??:0
13 0x0000000000092ea0 PMPI_Init() ??:0
14 0x00000000004009b6 main() ??:0
15 0x000000000001ed5d __libc_start_main() ??:0
16 0x00000000004008c9 _start() ??:0
===================
==== backtrace ====
2 0x0000000000056cdc mxm_handle_error()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_root/src/h
pcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:641
3 0x0000000000056e4c mxm_error_signal_handler()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_ro
ot/src/hpcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:616
4 0x00000000000326a0 killpg() ??:0
5 0x00000000000b82cb base_bcol_basesmuma_setup_library_buffers()
??:0
6 0x00000000000969e3 hmca_bcol_basesmuma_comm_query() ??:0
7 0x0000000000032ee3 hmca_coll_ml_tree_hierarchy_discovery()
coll_ml_module.c:0
8 0x000000000002fda2 hmca_coll_ml_comm_query() ??:0
9 0x000000000006ace9 hcoll_create_context() ??:0
10 0x00000000000f9706 mca_coll_hcoll_comm_query() ??:0
11 0x00000000000f684e mca_coll_base_comm_select() ??:0
12 0x0000000000073fc4 ompi_mpi_init() ??:0
13 0x0000000000092ea0 PMPI_Init() ??:0
14 0x00000000004009b6 main() ??:0
15 0x000000000001ed5d __libc_start_main() ??:0
16 0x00000000004008c9 _start() ??:0
===================
--------------------------------------------------------------------------
mpirun noticed that process rank 1 with PID 14678 on node zo-fe1
exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
Thanks,
David
On 08/12/2015 10:42 AM, Deva wrote:
Hi David,
This issue is from hcoll library. This could be because of symbol
conflict with ml module. This is fixed recently in HCOLL. Can
you try with "-mca coll ^ml" and see if this workaround works in
your setup?
-Devendar
On Wed, Aug 12, 2015 at 9:30 AM, David Shrader <dshra...@lanl.gov
<mailto:dshra...@lanl.gov>> wrote:
Hello Gilles,
Thank you very much for the patch! It is much more complete
than mine. Using that patch and re-running autogen.pl
<http://autogen.pl>, I am able to build 1.8.8 with
'./configure --with-hcoll' without errors.
I do have issues when it comes to running 1.8.8 with hcoll
built in, however. In my quick sanity test of running a basic
parallel hello world C program, I get the following:
[dshrader@zo-fe1 tests]$ mpirun -n 2 ./a.out
App launch reported: 1 (out of 1) daemons - 2 (out of 2) procs
[1439390789.039197] [zo-fe1:31354:0] shm.c:65 MXM
WARN Could not open the KNEM device file at /dev/knem : No
such file or direc
tory. Won't use knem.
[1439390789.040265] [zo-fe1:31353:0] shm.c:65 MXM
WARN Could not open the KNEM device file at /dev/knem : No
such file or direc
tory. Won't use knem.
[zo-fe1:31353:0] Caught signal 11 (Segmentation fault)
[zo-fe1:31354:0] Caught signal 11 (Segmentation fault)
==== backtrace ====
2 0x0000000000056cdc mxm_handle_error()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_root/src/h
pcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:641
3 0x0000000000056e4c mxm_error_signal_handler()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_ro
ot/src/hpcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:616
4 0x00000000000326a0 killpg() ??:0
5 0x00000000000b91eb
base_bcol_basesmuma_setup_library_buffers() ??:0
6 0x00000000000969e3 hmca_bcol_basesmuma_comm_query() ??:0
7 0x0000000000032ee3 hmca_coll_ml_tree_hierarchy_discovery()
coll_ml_module.c:0
8 0x000000000002fda2 hmca_coll_ml_comm_query() ??:0
9 0x000000000006ace9 hcoll_create_context() ??:0
10 0x00000000000fa626 mca_coll_hcoll_comm_query() ??:0
11 0x00000000000f776e mca_coll_base_comm_select() ??:0
12 0x0000000000074ee4 ompi_mpi_init() ??:0
13 0x0000000000093dc0 PMPI_Init() ??:0
14 0x00000000004009b6 main() ??:0
15 0x000000000001ed5d __libc_start_main() ??:0
16 0x00000000004008c9 _start() ??:0
===================
==== backtrace ====
2 0x0000000000056cdc mxm_handle_error()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_root/src/h
pcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:641
3 0x0000000000056e4c mxm_error_signal_handler()
/scrap/jenkins/workspace/hpc-power-pack/label/r-vmb-rhel6-u6-x86-64-MOFED-CHECKER/hpcx_ro
ot/src/hpcx-v1.3.336-gcc-OFED-1.5.4.1-redhat6.6-x86_64/mxm-v3.3/src/mxm/util/debug/debug.c:616
4 0x00000000000326a0 killpg() ??:0
5 0x00000000000b91eb
base_bcol_basesmuma_setup_library_buffers() ??:0
6 0x00000000000969e3 hmca_bcol_basesmuma_comm_query() ??:0
7 0x0000000000032ee3 hmca_coll_ml_tree_hierarchy_discovery()
coll_ml_module.c:0
8 0x000000000002fda2 hmca_coll_ml_comm_query() ??:0
9 0x000000000006ace9 hcoll_create_context() ??:0
10 0x00000000000fa626 mca_coll_hcoll_comm_query() ??:0
11 0x00000000000f776e mca_coll_base_comm_select() ??:0
12 0x0000000000074ee4 ompi_mpi_init() ??:0
13 0x0000000000093dc0 PMPI_Init() ??:0
14 0x00000000004009b6 main() ??:0
15 0x000000000001ed5d __libc_start_main() ??:0
16 0x00000000004008c9 _start() ??:0
===================
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 31353 on node
zo-fe1 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
I do not get this message with only 1 process.
I am using hcoll 3.2.748. Could this be an issue with hcoll
itself or something with my ompi build?
Thanks,
David
On 08/12/2015 12:26 AM, Gilles Gouaillardet wrote:
Thanks David,
i made a PR for the v1.8 branch at
https://github.com/open-mpi/ompi-release/pull/492
the patch is attached (it required some back-porting)
Cheers,
Gilles
On 8/12/2015 4:01 AM, David Shrader wrote:
I have cloned Gilles' topic/hcoll_config branch and, after
running autogen.pl <http://autogen.pl>, have found that
'./configure --with-hcoll' does indeed work now. I used
Gilles' branch as I wasn't sure how best to get the pull
request changes in to my own clone of master. It looks like
the proper checks are happening, too:
--- MCA component coll:hcoll(m4 configuration macro)
checking for MCA component coll:hcollcompile mode... dso
checking --with-hcollvalue... simple ok (unspecified)
checking hcoll/api/hcoll_api.h usability... yes
checking hcoll/api/hcoll_api.h presence... yes
checking for hcoll/api/hcoll_api.h... yes
looking for library without search path
checking for library containing hcoll_get_version... -lhcoll
checking if MCA component coll:hcollcan compile... yes
I haven't checked whether or not Open MPI builds
successfully as I don't have much experience running off of
the latest source. For now, I think I will try to generate
a patch to the 1.8.8 configure script and see if that works
as expected.
Thanks,
David
On 08/11/2015 06:34 AM, Jeff Squyres (jsquyres) wrote:
On Aug 11, 2015, at 1:39 AM, Åke Sandgren<ake.sandg...@hpc2n.umu.se>
<mailto:ake.sandg...@hpc2n.umu.se> wrote:
Please fix the hcoll test (and code) to be correct.
Any configure test that adds /usr/lib and/or /usr/include to any
compile flags is broken.
+1
Gilles filedhttps://github.com/open-mpi/ompi/pull/796; I just added
some comments to it.
--
David Shrader
HPC-3 High Performance Computer Systems
Los Alamos National Lab
Email: dshrader <at>lanl.gov <http://lanl.gov>
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Los Alamos National Lab
Email: dshrader <at>lanl.gov <http://lanl.gov>
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--
-Devendar
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HPC-3 High Performance Computer Systems
Los Alamos National Lab
Email: dshrader <at>lanl.gov <http://lanl.gov>
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HPC-3 High Performance Computer Systems
Los Alamos National Lab
Email: dshrader <at> lanl.gov
