Henry,
First, you could/should use mpicc instead of the cc cray compiler
I also noted
gfortran Linker Flags : -pthread -I/global/homes/h/hlovelac/BMAD/bmad_
dist_2018_0724/production/lib -Wl,-rpath -Wl,/global/homes/h/hlovelac/
BMAD/bmad_dist_2018_0724/production/lib -Wl,--enable-new-dtags -L/global
/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/production/lib -lmpi_
usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi;-lX11
It should be '-lmpi -lX11' instead of '-lmpi;-lX11'
The linker flags suggest Open MPI is installed in /global/homes/h/
hlovelac/BMAD/bmad_dist_2018_0724/production/lib, but your LD_LIBRARY_
PATH suggests it is in
$HOME/BMAD/bmad_dist_2018_0717/production/lib
(note 0724 vs 0717)
Also, keep in mind LD_LIBRARY_PATH is only used at runtime in order to
resolve dependencies.
The linker does *not* use LD_LIBRARY_PATH.
IIRC, it uses LIBRARY_PATH, but the preferred way is to use the -L<path>
argument.
If your problem persists, I suggest you get the full command line that
is failing.
(It should invoke mpifort instead gfortran or cc). Then you can copy/
paste the mpifort command, add the
-showme parameter, and run it manually so we can understand what is
really hapenning under the(cmake) hood.
Cheers,
Gilles
----- Original Message -----
Hi,
I am receiving these errors when building with OpenMPI on the
NERSC system.
Building directory: util_programs
-- The C compiler identification is GNU 7.1.0
-- The CXX compiler identification is GNU 7.1.0
-- Cray Programming Environment 2.5.12 C
-- Check for working C compiler: /opt/cray/pe/craype/2.5.12/bin/cc
-- Check for working C compiler: /opt/cray/pe/craype/2.5.12/bin/cc -
- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Cray Programming Environment 2.5.12 CXX
-- Check for working CXX compiler: /opt/cray/pe/craype/2.5.12/bin/CC
-- Check for working CXX compiler: /opt/cray/pe/craype/2.5.12/bin/CC
-- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The Fortran compiler identification is GNU 7.1.0
-- Check for working Fortran compiler: /global/homes/h/hlovelac/BMAD
/bmad_dist_2018_0724/production/bin/mpifort
-- Check for working Fortran compiler: /global/homes/h/hlovelac/BMAD
/bmad_dist_2018_0724/production/bin/mpifort -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /global/homes/h/hlovelac/BMAD/bmad_dist_2018_
0724/production/bin/mpifort supports Fortran 90
-- Checking whether /global/homes/h/hlovelac/BMAD/bmad_dist_2018_
0724/production/bin/mpifort supports Fortran 90 -- yes
Build type : Production
Linking with release : /global/homes/h/hlovelac/BMAD/bmad_dist_2018_
0724 (Off-site Distribution)
C Compiler : /opt/cray/pe/craype/2.5.12/bin/cc
Fortran Compiler : /global/homes/h/hlovelac/BMAD/bmad_dist_2018_
0724/production/bin/mpifort
Plotting Libraries : pgplot
OpenMP Support : Not Enabled
MPI Support : Enabled
FFLAGS :
gfortran Compiler Flags : -Df2cFortran -DCESR_UNIX -DCESR_LINUX -u -
traceback -cpp -fno-range-check -fdollar-ok -fbacktrace -Bstatic -ffree-
line-length-none -DCESR_PGPLOT -I/global/homes/h/hlovelac/BMAD/bmad_dist
_2018_0724/production/include -pthread -I/global/homes/h/hlovelac/BMAD/
bmad_dist_2018_0724/production/lib -fPIC -O2
gfortran Linker Flags : -pthread -I/global/homes/h/hlovelac/BMAD/
bmad_dist_2018_0724/production/lib -Wl,-rpath -Wl,/global/homes/h/
hlovelac/BMAD/bmad_dist_2018_0724/production/lib -Wl,--enable-new-dtags
-L/global/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/production/lib -lmpi
_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi;-lX11
SHARED DEPS :
-- Configuring done
-- Generating done
-- Build files have been written to: /global/homes/h/hlovelac/BMAD/
bmad_dist_2018_0724/util_programs/production
Scanning dependencies of target compare_tracking_methods_text-exe
Scanning dependencies of target compare_tracking_methods_plot-exe
Scanning dependencies of target f77_to_f90-exe
Scanning dependencies of target util_programs
Scanning dependencies of target lattice_cleaner-exe
Scanning dependencies of target bmad_to_gpt-exe
Scanning dependencies of target bmad_to_mad_sad_and_xsif-exe
Scanning dependencies of target sad_to_bmad_postprocess-exe
Scanning dependencies of target aspea2-exe
Scanning dependencies of target bmad_to_csrtrack-exe
Scanning dependencies of target ansga2-exe
Scanning dependencies of target bmad_to_blender-exe
Scanning dependencies of target bmad_to_autocad-exe
Scanning dependencies of target element_attributes-exe
Scanning dependencies of target wake_fit-exe
Scanning dependencies of target envelope_ibs-exe
[ 1%] Building Fortran object CMakeFiles/compare_tracking_methods_
text-exe.dir/compare_tracking_methods_text/compare_tracking_methods_text.
f90.o
[ 3%] Building Fortran object CMakeFiles/f77_to_f90-exe.dir/f77_to_
f90/f77_to_f90.f90.o
[ 5%] Building Fortran object CMakeFiles/compare_tracking_methods_
plot-exe.dir/compare_tracking_methods_plot/compare_tracking_methods_plot.
f90.o
[ 7%] Building Fortran object CMakeFiles/lattice_cleaner-exe.dir/
lattice_cleaner/lattice_cleaner.f90.o
[ 9%] Building Fortran object CMakeFiles/sad_to_bmad_postprocess-
exe.dir/sad_to_bmad/sad_to_bmad_postprocess.f90.o
[ 11%] Building Fortran object CMakeFiles/bmad_to_gpt-exe.dir/bmad_
to_gpt/bmad_to_gpt.f90.o
[ 13%] Building Fortran object CMakeFiles/bmad_to_mad_sad_and_xsif-
exe.dir/bmad_to_mad_sad_and_xsif/bmad_to_mad_sad_and_xsif.f90.o
[ 15%] Building Fortran object CMakeFiles/bmad_to_csrtrack-exe.dir/
bmad_to_csrtrack/bmad_to_csrtrack.f90.o
[ 16%] Building Fortran object CMakeFiles/element_attributes-exe.dir
/element_attributes/element_attributes.f90.o
[ 22%] Building Fortran object CMakeFiles/bmad_to_autocad-exe.dir/
bmad_to_autocad/bmad_to_autocad.f90.o
[ 22%] Building Fortran object CMakeFiles/wake_fit-exe.dir/wake_fit/
wake_fit.f90.o
[ 22%] Building Fortran object CMakeFiles/envelope_ibs-exe.dir/
envelope_ibs/envelope_ibs.f90.o
[ 24%] Building Fortran object CMakeFiles/bmad_to_blender-exe.dir/
bmad_to_blender/bmad_to_blender.f90.o
[ 28%] Building CXX object CMakeFiles/ansga2-exe.dir/apisa/nsga2/
nsga2_io.cpp.o
[ 30%] Building CXX object CMakeFiles/ansga2-exe.dir/apisa/nsga2/
nsga2.cpp.o
[ 32%] Building Fortran object CMakeFiles/util_programs.dir/modules/
pisa_mod.f90.o
[ 32%] Building CXX object CMakeFiles/aspea2-exe.dir/apisa/spea2/
spea2_io.cpp.o
[ 33%] Building CXX object CMakeFiles/aspea2-exe.dir/apisa/spea2/
spea2_functions.cpp.o
[ 37%] Building CXX object CMakeFiles/aspea2-exe.dir/apisa/spea2/
spea2.cpp.o
[ 39%] Building Fortran object CMakeFiles/util_programs.dir/modules/
moga_struct_mod.f90.o
[ 39%] Building Fortran object CMakeFiles/util_programs.dir/modules/
make_pseudoinverse_mod.f90.o
[ 43%] Building CXX object CMakeFiles/ansga2-exe.dir/apisa/nsga2/
nsga2_functions.cpp.o
[ 43%] Building Fortran object CMakeFiles/util_programs.dir/modules/
four_mod.f90.o
/global/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/util_programs/f77_
to_f90/f77_to_f90.f90:725:0:
if (there) line(ix_end:) = 'call ' // line(ix_end:)
Warning: '__builtin_memset': specified size 18446744073709551611
exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
/global/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/util_programs/f77_
to_f90/f77_to_f90.f90:755:0:
if (there) line(ix_end:) = 'call ' // line(ix_end:)
Warning: '__builtin_memset': specified size 18446744073709551611
exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
[ 45%] Building Fortran object CMakeFiles/util_programs.dir/modules/
crm_mod.f90.o
[ 47%] Building Fortran object CMakeFiles/util_programs.dir/modules/
adts_mod.f90.o
[ 49%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/compare_tracking_methods_text
[ 50%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/element_attributes
[ 52%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/bmad_to_blender
[ 54%] Linking CXX executable /global/homes/h/hlovelac/BMAD/bmad_
dist_2018_0724/production/bin/ansga2
[ 56%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/lattice_cleaner
[ 58%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/wake_fit
[ 60%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/bmad_to_mad_sad_and_xsif
[ 62%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/f77_to_f90
[ 64%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/bmad_to_gpt
/usr/bin/ld: cannot find -lmpi_usempif08
/usr/bin/ld: cannot find -lmpi_usempi_ignore_tkr
/usr/bin/ld: cannot find -lmpi_mpifh
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -lX11
collect2: error: ld returned 1 exit status
CMakeFiles/ansga2-exe.dir/build.make:146: recipe for target '/global
/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/production/bin/ansga2' failed
gmake[2]: *** [/global/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/
production/bin/ansga2] Error 1
CMakeFiles/Makefile2:447: recipe for target 'CMakeFiles/ansga2-exe.
dir/all' failed
gmake[1]: *** [CMakeFiles/ansga2-exe.dir/all] Error 2
gmake[1]: *** Waiting for unfinished jobs....
[ 66%] Linking CXX executable /global/homes/h/hlovelac/BMAD/bmad_
dist_2018_0724/production/bin/aspea2
[ 67%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/bmad_to_csrtrack
[ 69%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/bmad_to_autocad
/usr/bin/ld: cannot find -lmpi_usempif08
/usr/bin/ld: cannot find -lmpi_usempi_ignore_tkr
/usr/bin/ld: cannot find -lmpi_mpifh
/usr/bin/ld: cannot find -lmpi
/usr/bin/ld: cannot find -lX11
collect2: error: ld returned 1 exit status
CMakeFiles/aspea2-exe.dir/build.make:146: recipe for target '/global
/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/production/bin/aspea2' failed
gmake[2]: *** [/global/homes/h/hlovelac/BMAD/bmad_dist_2018_0724/
production/bin/aspea2] Error 1
CMakeFiles/Makefile2:484: recipe for target 'CMakeFiles/aspea2-exe.
dir/all' failed
gmake[1]: *** [CMakeFiles/aspea2-exe.dir/all] Error 2
[ 73%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/sad_to_bmad_postprocess
[ 73%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/compare_tracking_methods_plot
[ 73%] Built target element_attributes-exe
[ 73%] Built target wake_fit-exe
[ 73%] Built target f77_to_f90-exe
[ 75%] Building Fortran object CMakeFiles/util_programs.dir/modules/
dynap_mod.f90.o
[ 75%] Built target bmad_to_blender-exe
[ 75%] Built target compare_tracking_methods_text-exe
[ 75%] Built target lattice_cleaner-exe
[ 75%] Built target bmad_to_gpt-exe
[ 75%] Built target bmad_to_autocad-exe
[ 75%] Built target bmad_to_mad_sad_and_xsif-exe
[ 75%] Built target bmad_to_csrtrack-exe
[ 77%] Linking Fortran executable /global/homes/h/hlovelac/BMAD/bmad
_dist_2018_0724/production/bin/envelope_ibs
[ 77%] Built target sad_to_bmad_postprocess-exe
[ 77%] Built target compare_tracking_methods_plot-exe
[ 79%] Building Fortran object CMakeFiles/util_programs.dir/modules/
custom_dynamic_aperture_mod.f90.o
[ 79%] Built target envelope_ibs-exe
[ 84%] Building Fortran object CMakeFiles/util_programs.dir/modules/
namelist_da.f90.o
[ 84%] Building Fortran object CMakeFiles/util_programs.dir/modules/
namelist_general.f90.o
[ 84%] Building Fortran object CMakeFiles/util_programs.dir/modules/
linear_aperture_mod.f90.o
[ 86%] Building Fortran object CMakeFiles/util_programs.dir/modules/
namelist_moga.f90.o
[ 88%] Linking Fortran static library /global/homes/h/hlovelac/BMAD/
bmad_dist_2018_0724/production/lib/libutil_programs.a
[ 88%] Built target util_programs
Makefile:83: recipe for target 'all' failed
gmake: *** [all] Error 2
Error in distribution build.
The build is not seeing the mpi libraries even though before the
build I defined
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:$HOME/BMAD/bmad_dist_2018_
0717/production/lib
Is this error from the MPIfort?
Thanks,
Henry
From: users <users-boun...@lists.open-mpi.org> on behalf of Brian
Smith <bsm...@systemfabricworks.com>
Sent: Monday, July 23, 2018 2:06:14 PM
To: Open MPI Users
Subject: Re: [OMPI users] Error in file base/plm_base_launch_support.
c: OPAL_HWLOC_TOPO
On Sat, Jul 21, 2018 at 9:13 PM, Gilles Gouaillardet
<gilles.gouaillar...@gmail.com> wrote:
> Brian,
>
> As Ralph already stated, this is likely a hwloc API issue.
> From debian9, you can
> lstopo --of xml | ssh debian8 lstopo --if xml -i -
>
> that will likely confirm the API error.
>
> If you are willing to get a bit more details, you can add some
printf
> in opal_hwloc_unpack (from opal/mca/hwloc/base/hwloc_base_dt.c) to
> figure out where exactly the failure occurs.
>
> Meanwhile, you can move forward by using the embedded hwloc on
both
> distros (--with-hwloc=internal or no --with-hwloc option at all).
>
>
> Note we strongly discourage you configure --with-FOO=/usr
> (it explicitly add /usr/include and /usr/lib[64] in the search
path,
> and might hide some other external libraries installed in a non
> standard location). In order to force the external hwloc lib
installed
> in the default location, --with-hwloc=external is what you need (
same
> thing applies to libevent and pmix)
Thank you for the advice. Removing --with-hwloc from the configure
statement corrected the problem.
>
>
> Cheers,
>
> Gilles
> On Sun, Jul 22, 2018 at 7:52 AM r...@open-mpi.org <r...@open-mpi.org
> wrote:
>>
>> More than likely the problem is the difference in hwloc versions
- sounds like the topology to/from xml is different between the two
versions, and the older one doesn’t understand the new one.
>>
>> > On Jul 21, 2018, at 12:04 PM, Brian Smith <bsmith@
systemfabricworks.com> wrote:
>> >
>> > Greetings,
>> >
>> > I'm having trouble getting openmpi 2.1.2 to work when launching
a
>> > process from debian 8 on a remote debian 9 host. To keep things
simple
>> > in this example, I'm just launching date on the remote host.
>> >
>> > deb8host$ mpirun -H deb9host date
>> > [deb8host:01552] [[32763,0],0] ORTE_ERROR_LOG: Error in file
>> > base/plm_base_launch_support.c at line 954
>> >
>> > It works fine when executed from debian 9:
>> > deb9host$ mpirun -H deb8host date
>> > Sat Jul 21 13:40:43 CDT 2018
>> >
>> > Also works when executed from debian 8 against debian 8:
>> > deb8host:~$ mpirun -H deb8host2 date
>> > Sat Jul 21 13:55:57 CDT 2018
>> >
>> > The failure results from an error code returned by:
>> > opal_dss.unpack(buffer, &topo, &idx, OPAL_HWLOC_TOPO)
>> >
>> > openmpi was built with the same configure flags on both hosts.
>> >
>> > --prefix=$(PREFIX) \
>> > --with-verbs \
>> > --with-libfabric \
>> > --disable-silent-rules \
>> > --with-hwloc=/usr \
>> > --with-libltdl=/usr \
>> > --with-devel-headers \
>> > --with-slurm \
>> > --with-sge \
>> > --without-tm \
>> > --disable-heterogeneous \
>> > --with-contrib-vt-flags=--disable-iotrace \
>> > --sysconfdir=$(PREFIX)/etc \
>> > --libdir=$(PREFIX)/lib \
>> > --includedir=$(PREFIX)/include
>> >
>> >
>> > deb9host libhwloc and libhwloc-plugins is 1.11.5-1
>> > deb8host libhwloc and libhwloc-plugins is 1.10.0-3
>> >
>> > I've been trying to debug this for the past few days and would
>> > appreciate any help on determining why this failure is
occurring
>> > and/or resolving the problem.
>> >
>> > --
>> > Brian T. Smith
>> > System Fabric Works
>> > Senior Technical Staff
>> > bsm...@systemfabricworks.com
>> > GPG Key: B3C2C7B73BA3CD7F
>> > _______________________________________________
>> > users mailing list
>> > users@lists.open-mpi.org
>> > https://lists.open-mpi.org/mailman/listinfo/users
users Info Page - Open MPI
lists.open-mpi.org
General user information and questions about Open MPI. ==> Users
Archives Using users: To post a message to all the list members, send
email to users@lists.open-mpi.org.
>>
>> _______________________________________________
>> users mailing list
>> users@lists.open-mpi.org
>> https://lists.open-mpi.org/mailman/listinfo/users
> _______________________________________________
> users mailing list
> users@lists.open-mpi.org
> https://lists.open-mpi.org/mailman/listinfo/users
--
Brian T. Smith
System Fabric Works
Senior Technical Staff
bsm...@systemfabricworks.com
GPG Key: B3C2C7B73BA3CD7F
_______________________________________________
users mailing list
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https://lists.open-mpi.org/mailman/listinfo/users
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