Building OPENCMISS Iron after setting up arch path raises problem with gdcm

vraj004 commented 4 years ago

I tried to compile opencmiss iron (ubuntu 18.04, gcc-9, gfortran 9) by first setting up arch path:

cd setup-build
cmake -DOPENCMISS_ROOT=../opencmiss -DOPENCMISS_LIBRARIES=iron .-DOPENCMISS_PERFORM_INITIAL_BUILD=False ./setup
make VERBOSE=1
cd ../../build/manage/release

cmake .

make create_config
make build_config

The compiler fails at OC_GDCM:

Scanning dependencies of target OC_GDCM-ABI [ 15%] Creating directories for 'OC_GDCM-ABI' [ 17%] No download step for 'OC_GDCM-ABI' [ 17%] No patch step for 'OC_GDCM-ABI' [ 17%] No update step for 'OC_GDCM-ABI' [ 17%] Performing configure step for 'OC_GDCM-ABI' -- OC_GDCM-ABI configure command succeeded. See also /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-configure-*.log [ 17%] Performing build step for 'OC_GDCM-ABI' CMake Error at extproj/stamp/OC_GDCM-ABI-build-Release.cmake:49 (message): Command failed: 2

'/usr/local/bin/cmake' '--build' '/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release' '--' '-j8'

See also

/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-build-*.log

CMakeFiles/OC_GDCM-ABI.dir/build.make:114: recipe for target '/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-build' failed make[6]: *** [/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/build/x86_64_linux/gnu-C9.0-gnu-F9.0/no_mpi/dependencies/gdcm-abi/release/extproj/stamp/OC_GDCM-ABI-build] Error 1 CMakeFiles/Makefile2:3104: recipe for target 'CMakeFiles/OC_GDCM-ABI.dir/all' failed

vraj004 commented 4 years ago

Further examination of the compiler error inside the gdcm-abi folder: [ 7%] Built target gdcmCommon [ 7%] Building CXX object Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/gdcmCReader.cxx.o In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h:21, from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmFile.h:19, from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmReader.h:19, from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Wrapping/C/gdcmCReader.cxx:12: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmElement.h:606:26: error: declaration of ‘class gdcm::Element<4096, TVM>’ ambiguates earlier template instantiation for ‘class gdcm::Element<4096, 218367>’ [-fpermissive] 606 | template class Element<VR::OB, TVM>; | ^~~~~~~~ /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmElement.h:612:26: error: declaration of ‘class gdcm::Element<16384, TVM>’ ambiguates earlier template instantiation for ‘class gdcm::Element<16384, 218367>’ [-fpermissive] 612 | template class Element<VR::OW, TVM>; | ^~~~~~~~ /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/gdcm-abi/Source/DataStructureAndEncodingDefinition/gdcmElement.h:612:26: error: declaration of ‘class gdcm::Element<16384, TVM>’ ambiguates earlier template instantiation for ‘class gdcm::Element<4096, 218367>’ [-fpermissive] Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/build.make:62: recipe for target 'Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/gdcmCReader.cxx.o' failed make[2]: [Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/gdcmCReader.cxx.o] Error 1 CMakeFiles/Makefile2:113: recipe for target 'Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/all' failed make[1]: [Wrapping/C/CMakeFiles/gdcmCWRAPPER.dir/all] Error 2 M

chrispbradley commented 4 years ago

Hi Vijay, yes, whilst gcc-9 fixes the internal compiler fault it brings in additional problems in that some of the external libraries do not build with it because they are too old. GDCM above is not required by iron so you can turn it off. Indeed, go to your configs directory and edit OpenCMISSLocalConfig.cmake and set

set(OC_USE_CLANG OFF) set(OC_USE_CSIM OFF) set(OC_USE_LLVM OFF) set(OC_USE_ZINC OFF) set(CELLML_WITH_CSIM NO)

It should then build with gcc-9

vraj004 commented 4 years ago

Why does this error not pop up when setting up opencmiss iron with the default settings - without setting the arch paths?

vraj004 commented 4 years ago

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include | ^~~ compilation terminated. make[9]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: Waiting for unfinished jobs.... make[7]: [all] Error 2

sgenie68 commented 4 years ago

What MPI do you use there?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 18:28, Vijay Rajagopal wrote:

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include | ^~~ compilation terminated. make[9]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: Waiting for unfinished jobs.... make[7]: [all] Error 2

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vraj004 commented 4 years ago

Mpich

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From: sgenie68 notifications@github.com Sent: Sunday, November 24, 2019 5:03:12 PM To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au; Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

What MPI do you use there?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 24/11/19 18:28, Vijay Rajagopal wrote:

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include | ^~~ compilation terminated. make[9]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: Waiting for unfinished jobs.... make[7]: [all] Error 2

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chrispbradley commented 4 years ago

Why does this error not pop up when setting up opencmiss iron with the default settings - without setting the arch paths?

Hi Vijay, I'll speculate that when you do the setup you specify iron only libraries and therefore it doesn't build zinc and therefore the zinc dependencies.

chrispbradley commented 4 years ago

Hi Vijay, It can't find mpich for some reason. What do you get when you do a which mpiexec? mpif90 --version? mpicc --version? Also have you installed libmpich-dev?

vraj004 commented 4 years ago

Hi Chris

I have installed libmpich-dev.

I get gcc-9 when checking version of mpicc and mpif90. I get the following error for mpiexec:

[mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided

[mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

[mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: Chris Bradley notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Sunday, 24 November 2019 at 6:55 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi Vijay, It can't find mpich for some reason. What do you get when you do a which mpiexec? mpif90 --version? mpicc --version? Also have you installed libmpich-dev?

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chrispbradley commented 4 years ago

Hi Vijay, is that output for

which mpiexec

or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH?

sgenie68 commented 4 years ago

The problem might be related to the conflicts between anaconda-installed version of mpich and the system-configured one

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 22:28, Chris Bradley wrote:

Hi Vijay, is that output for

which mpiexec

or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH?

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vraj004 commented 4 years ago

HI Gene, I am now running a linux virtual machine without anaconda. So this is an issue on linux ubuntu 18.04

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Sunday, 24 November 2019 at 8:35 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

The problem might be related to the conflicts between anaconda-installed version of mpich and the system-configured one

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 24/11/19 22:28, Chris Bradley wrote:

Hi Vijay, is that output for

which mpiexec

or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH?

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vraj004 commented 4 years ago

HI Chris, I did env | grep PATH and this is what I get:

PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

The previous output was for running mpiexec. I ran mpiexec--version and this is what I get: HYDRA build details:

Version:                                 3.3a2

Release Date:                            Sun Nov 13 09:12:11 MST 2016

CC:                              gcc   -Wl,-Bsymbolic-functions -Wl,-z,relro

CXX:                             g++   -Wl,-Bsymbolic-functions -Wl,-z,relro

F77:                             gfortran  -Wl,-Bsymbolic-functions -Wl,-z,relro

F90:                             gfortran  -Wl,-Bsymbolic-functions -Wl,-z,relro

Configure options:                       '--disable-option-checking' '--prefix=/usr' '--build=x86_64-linux-gnu' '--includedir=${prefix}/include' '--mandir=${prefix}/share/man' '--infodir=${prefix}/share/info' '--sysconfdir=/etc' '--localstatedir=/var' '--disable-silent-rules' '--libdir=${prefix}/lib/x86_64-linux-gnu' '--libexecdir=${prefix}/lib/x86_64-linux-gnu' '--disable-maintainer-mode' '--disable-dependency-tracking' '--with-libfabric' '--enable-shared' '--enable-fortran=all' '--disable-rpath' '--disable-wrapper-rpath' '--sysconfdir=/etc/mpich' '--libdir=/usr/lib/x86_64-linux-gnu' '--includedir=/usr/include/mpich' '--docdir=/usr/share/doc/mpich' '--with-hwloc-prefix=system' '--enable-checkpointing' '--with-hydra-ckpointlib=blcr' 'CPPFLAGS= -Wdate-time -D_FORTIFY_SOURCE=2 -I/build/mpich-O9at2o/mpich-3.3~a2/src/mpl/include -I/build/mpich-O9at2o/mpich-3.3~a2/src/mpl/include -I/build/mpich-O9at2o/mpich-3.3~a2/src/openpa/src -I/build/mpich-O9at2o/mpich-3.3~a2/src/openpa/src -D_REENTRANT -I/build/mpich-O9at2o/mpich-3.3~a2/src/mpi/romio/include' 'CFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security -O2' 'CXXFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security -O2' 'FFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -O2' 'FCFLAGS= -g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -O2' 'build_alias=x86_64-linux-gnu' 'MPICHLIB_CFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security' 'MPICHLIB_CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2' 'MPICHLIB_CXXFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong -Wformat -Werror=format-security' 'MPICHLIB_FFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong' 'MPICHLIB_FCFLAGS=-g -O2 -fdebug-prefix-map=/build/mpich-O9at2o/mpich-3.3~a2=. -fstack-protector-strong' 'LDFLAGS=-Wl,-Bsymbolic-functions -Wl,-z,relro' 'FC=gfortran' 'F77=gfortran' 'MPILIBNAME=mpich' '--cache-file=/dev/null' '--srcdir=.' 'CC=gcc' 'LIBS=' 'MPLLIBNAME=mpl'

Process Manager:                         pmi

Launchers available:                     ssh rsh fork slurm ll lsf sge manual persist

Topology libraries available:            hwloc

Resource management kernels available:   user slurm ll lsf sge pbs cobalt

Checkpointing libraries available:       blcr

Demux engines available:                 poll select

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: Chris Bradley notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Sunday, 24 November 2019 at 8:28 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi Vijay, is that output for

which mpiexec

or for when you run mpiexec? Something is not right. Can you send the output for env | grep PATH?

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sgenie68 commented 4 years ago

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

vraj004 commented 4 years ago

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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sgenie68 commented 4 years ago

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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vraj004 commented 4 years ago

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/OpenCMISS/iron/issues/187?email_source=notifications&email_token=AAGX4ZPF4WC64XU6B3D3VBLQVLY7VA5CNFSM4JQ5FI52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAVW4I#issuecomment-557931377, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAGX4ZLLPUVLZAW2LPQMD5LQVLY7VANCNFSM4JQ5FI5Q.

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sgenie68 commented 4 years ago

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo:

sudo mpiexec

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 25/11/19 11:01, Vijay Rajagopal wrote:

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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vraj004 commented 4 years ago

Hi Gene, here it is:

[mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided

[mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

[mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo:

sudo mpiexec

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 11:01, Vijay Rajagopal wrote:

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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sgenie68 commented 4 years ago

Ok, you need to give it an executable - something that runs under mpi control, even a simple

mpiexec -np 4 hostname

would do

Cheers, gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 25/11/19 14:45, Vijay Rajagopal wrote:

Hi Gene, here it is:

[mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided

[mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

[mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo:

sudo mpiexec

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 11:01, Vijay Rajagopal wrote:

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

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From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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vraj004 commented 4 years ago

Yes, sorry that works

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 12:48 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Ok, you need to give it an executable - something that runs under mpi control, even a simple

mpiexec -np 4 hostname

would do

Cheers, gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 14:45, Vijay Rajagopal wrote:

Hi Gene, here it is:

[mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided

[mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

[mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo:

sudo mpiexec

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 11:01, Vijay Rajagopal wrote:

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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sgenie68 commented 4 years ago

Good, now do:

which mpiexec

and see where it leads you to

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 25/11/19 15:00, Vijay Rajagopal wrote:

Yes, sorry that works

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 12:48 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Ok, you need to give it an executable - something that runs under mpi control, even a simple

mpiexec -np 4 hostname

would do

Cheers, gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 14:45, Vijay Rajagopal wrote:

Hi Gene, here it is:

[mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided

[mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

[mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo:

sudo mpiexec

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 11:01, Vijay Rajagopal wrote:

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>

On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E:

vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/|

twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal http://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>>>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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vraj004 commented 4 years ago

Hi Gene,

/usr/bin/mpiexec

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 1:01 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Good, now do:

which mpiexec

and see where it leads you to

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 25/11/19 15:00, Vijay Rajagopal wrote:

Yes, sorry that works

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal<http://twitter.com/vj_rajagopal>

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 12:48 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Ok, you need to give it an executable - something that runs under mpi control, even a simple

mpiexec -np 4 hostname

would do

Cheers, gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>

On 25/11/19 14:45, Vijay Rajagopal wrote:

Hi Gene, here it is:

[mpiexec@4000v-udp14-l] set_default_values (ui/mpich/utils.c:1529): no executable provided

[mpiexec@4000v-udp14-l] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

[mpiexec@4000v-udp14-l] main (ui/mpich/mpiexec.c:149): error parsing parameters

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

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From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 9:18 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, sorry to bombard you with the questions - but can you try execute mpiexec with sudo:

sudo mpiexec

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>

On 25/11/19 11:01, Vijay Rajagopal wrote:

I simply installed libmpich-dev via sudo apt install libmpich-dev

What else should I do?

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

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From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:58 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you configure MPICH without BLCR or any other checkpointing support?

Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

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On 25/11/19 10:49, Vijay Rajagopal wrote:

I simply typed: mpiexec

Best wishes

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E:

vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology

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From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 8:47 am To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Hi, Vijay

Could you give me the command line you used when you ran mpiexec?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w:

https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html<https://www.auckland.ac.nz/en/abi.html>>>>

On 24/11/19 21:45, Vijay Rajagopal wrote:

HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1740): setting default values failed

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sgenie68 commented 4 years ago

Vijay, can you run the following code before cmake:

export FC=mpif90 export CC=mpicc export CXX=mpicxx

and then run cmake stuff

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 24/11/19 18:28, Vijay Rajagopal wrote:

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include | ^~~ compilation terminated. make[9]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: Waiting for unfinished jobs.... make[7]: [all] Error 2

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vraj004 commented 4 years ago

The system stalls trying to find MPICH when I do that.

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 2:16 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you run the following code before cmake:

export FC=mpif90 export CC=mpicc export CXX=mpicxx

and then run cmake stuff

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 24/11/19 18:28, Vijay Rajagopal wrote:

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57: /home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21: fatal error: mpi.h: No such file or directory 194 | #include | ^~~ compilation terminated. make[9]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: Waiting for unfinished jobs.... make[7]: [all] Error 2

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sgenie68 commented 4 years ago

Hi, Vijay

Would it be possible to run cmake like that:

strace cmake 2>output_file

and send this output file to me?

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html

On 26/11/19 12:07, Vijay Rajagopal wrote:

The system stalls trying to find MPICH when I do that.

Vijay Rajagopal | Senior Lecturer Department of Biomedical Engineering | Melbourne School of Engineering Building 261, 197-203 Bouverie Street The University of Melbourne, Victoria 3010 Australia T: +61 3 834 41281 E: vijay.rajagopal@unimelb.edu.aumailto:vijay.rajagopal@unimelb.edu.au Cell Structure and Mechanobiology Grouphttps://biomedical.eng.unimelb.edu.au/cell-structure-mechanobiology/| twitter.com/vj_rajagopalhttp://twitter.com/vj_rajagopal

From: sgenie68 notifications@github.com Reply to: OpenCMISS/iron reply@reply.github.com Date: Monday, 25 November 2019 at 2:16 pm To: OpenCMISS/iron iron@noreply.github.com Cc: Vijay Rajagopal vijay.rajagopal@unimelb.edu.au, Author author@noreply.github.com Subject: Re: [OpenCMISS/iron] Building OPENCMISS Iron after setting up arch path raises problem with gdcm (#187)

Vijay, can you run the following code before cmake:

export FC=mpif90 export CC=mpicc export CXX=mpicxx

and then run cmake stuff

Cheers, Gene

-- Scientific Software Specialist Auckland Bioengineering Institute The University of Auckland e: g.soudlenkov@auckland.ac.nz p: +64 9 3737599 ext 89834 c: +64 21 840 825 w: https://www.auckland.ac.nz/en/abi.html https://www.auckland.ac.nz/en/abi.html

On 24/11/19 18:28, Vijay Rajagopal wrote:

After setting the corresponding flags off as suggested (in OpenCMISSLocalConfig.cmake) I now get compilation error with OC_SCOTCH:

lex.yy.c: In function ‘scotchyy_init_buffer’: lex.yy.c:1566:48: warning: implicit declaration of function ‘fileno’ [-Wimplicit-function-declaration] In file included from

/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/bdgraph.c:57:

/home/unimelb.edu.au/vrajagopal/applications/opencmiss_install/opencmiss/src/dependencies/scotch/src/libscotch/common.h:194:21:

fatal error: mpi.h: No such file or directory 194 | #include | ^~~ compilation terminated. make[9]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/__/bdgraph.c.o] Error 1 make[8]: [src/libscotch/libptscotch/CMakeFiles/ptscotch.dir/all] Error 2 make[8]: Waiting for unfinished jobs.... make[7]: [all] Error 2

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OpenCMISS / iron

Building OPENCMISS Iron after setting up arch path raises problem with gdcm #187