MPI Issue

[David Parker]

Hi William,

You don't seem to have Fortran libraries. Have you installed gcc using brew install gcc? I that should include the Fortran libraries. Which MacOS are you running?

Cheers,
Dave

[William Yoon]

Hi Dave,

I am using MacOS (11.4). It is intel chip.
I've already un-installed and re-installed GCC by using "brew install gcc." without success...

Z-MacBook-Pro:~ A$ brew install gcc
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 2 taps (homebrew/core and homebrew/cask).
==> Updated Formulae
Updated 47 formulae.
==> Updated Casks
Updated 6 casks.

Warning: gcc 11.1.0_1 is already installed and up-to-date.
To reinstall 11.1.0_1, run:
brew reinstall gcc

[David Parker]

Have you done an xcode-select --install ?

If not uninstall gcc, do xcode-select --install and then install gcc again.

Sorry this is taking so long! I develop primarily on a Mac and it seems that MacOS is getting worse, development wise, every new release.

Cheers,
Dave

[William Yoon]

I appreciate all your help Dave.

I uninstalled gcc then did xcode-select --install then reinstalled gcc.
Unfortunately, I encountered same issue...


Z-MacBook-Pro:~ A$ xcode-select --install
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
Z-MacBook-Pro:~ A$ brew install gcc
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
==> Updated Formulae
Updated 10 formulae.

==> Downloading https://ghcr.io/v2/homebrew/core/gcc/manifests/11.1.0_1
Already downloaded: /Users/A/Library/Caches/Homebrew/downloads/f7bb8eeac80de9990fc7ff7ec216d4e1eb0cf861e852e8d62317f52eb667bb3b--gcc-11.1.0_1.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/gcc/bl ... 8e83ce46f4
Already downloaded: /Users/A/Library/Caches/Homebrew/downloads/7b6c50d89dfe506752f9adea32f7ef5943121783145a5f8e4c1a1b9fefdc140a--gcc--11.1.0_1.big_sur.bottle.tar.gz
==> Pouring gcc--11.1.0_1.big_sur.bottle.tar.gz
/usr/local/Cellar/gcc/11.1.0_1: 2,163 files, 460.2MB
Z-MacBook-Pro:~ A$ brew install open-mpi
==> Downloading https://ghcr.io/v2/homebrew/core/open-m ... ts/4.1.1_2
Already downloaded: /Users/A/Library/Caches/Homebrew/downloads/467c84611ee1e10e3019e70726660e44ed32f67dd172d18fa9ede03dddd2ff49--open-mpi-4.1.1_2.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/open-m ... :da310195e
Already downloaded: /Users/A/Library/Caches/Homebrew/downloads/fb40e3afddec91e3219c5b6ee06dfbf5c5f25c3fe23587d8aa76852a1b716486--open-mpi--4.1.1_2.big_sur.bottle.tar.gz
==> Pouring open-mpi--4.1.1_2.big_sur.bottle.tar.gz
/usr/local/Cellar/open-mpi/4.1.1_2: 760 files, 15.9MB
Z-MacBook-Pro:~ A$ brew doctor
Your system is ready to brew.
Z-MacBook-Pro:~ A$ cd ~/Desktop/CoronaryProject/Simulations/pulsatile_sim
Z-MacBook-Pro:pulsatile_sim A$ mpiexec -np 4 /usr/local/sv/svsolver/2021-06-15/bin/svsolver solver.inp
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib
Referenced from: /usr/local/sv/svsolver/2021-06-15/bin/svsolver
Reason: image not found
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib
Referenced from: /usr/local/sv/svsolver/2021-06-15/bin/svsolver
Reason: image not found
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib
Referenced from: /usr/local/sv/svsolver/2021-06-15/bin/svsolver
Reason: image not found
dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/10/libgfortran.5.dylib
Referenced from: /usr/local/sv/svsolver/2021-06-15/bin/svsolver
Reason: image not found
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 3 with PID 0 on node Z-MacBook-Pro exited on signal 6 (Abort trap: 6).

[Ryan DeGroff]

mpiexec -np 4 /usr/local/sv/svsolver/2021-06-15/bin/svsolver solver.inp

Hey Dave, I should have mentioned that using mpiexec through the command line has been the only way I have been able to run simulations. Will we be able to use the application user interface, or do we need to rely on command line execution?

[David Parker]

Hi Ryan,

You should be able to run simulations from the GUI. What MacOS are you using?

Try removing the files in $HOME/Library/Application Support/SimVascular.

Cheers,
Dave

[David Parker]

Hi William,

Post the output of

Code: Select all

locate libgfortran.5.dylib

On my Mac I get

Code: Select all

/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.5.dylib
/usr/local/lib/gcc/10/libgfortran.5.dylib
/usr/local/sv/svsolver/2021-06-15/lib/libgfortran.5.dylib

Cheers,
Dave

[Ryan DeGroff]

Hi Ryan,

You should be able to run simulations from the GUI. What MacOS are you using?

Try removing the files in $HOME/Library/Application Support/SimVascular.

Cheers,
Dave

I am using Mac OS BigSur v11.4. I removed the files in that application support folder for SimVascular like you described, but when I try running the simulation I get the following error, almost as if the GUI is explicitly looking for a folder for open-mpi version 4.0.5, but my version is 4.1.1

Simulation job 'ctest1_smooth' has failed with non-zero exit code 1.

--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30476] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30488] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30494] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30500] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30506] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30511] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30515] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
opal_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-opal-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
orte_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-orte-runtime: No such file or directory. Sorry!
--------------------------------------------------------------------------
--------------------------------------------------------------------------
Sorry! You were supposed to get help about:
mpi_init:startup:internal-failure
But I couldn't open the help file:
/usr/local/Cellar/open-mpi/4.0.5/share/openmpi/help-mpi-runtime.txt: No such file or directory. Sorry!
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[Ryans-MBP:30482] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[49875,1],0]
Exit code: 1
--------------------------------------------------------------------------

This was the same error that William got before, but I have fortran libraries and xcode command line tools since svSolver works in Terminal.

[William Yoon]

Hi William,

Post the output of

Code: Select all

locate libgfortran.5.dylib

On my Mac I get

Code: Select all

/usr/local/Cellar/gcc/10.2.0/lib/gcc/10/libgfortran.5.dylib
/usr/local/lib/gcc/10/libgfortran.5.dylib
/usr/local/sv/svsolver/2021-06-15/lib/libgfortran.5.dylib

Cheers,
Dave

Hi Dave,

Here is my output
Thanks!

Code: Select all

Z-MacBook-Pro:~ A$ locate libgfortran.5.dylib
/Applications/ParaView-5.9.0.app/Contents/Libraries/libgfortran.5.dylib
/usr/local/Cellar/gcc/11.1.0_1/lib/gcc/11/libgfortran.5.dylib
/usr/local/sv/svFSI/2021-05-03/lib/libgfortran.5.dylib
/usr/local/sv/svsolver/2021-06-15/lib/libgfortran.5.dylib
Z-MacBook-Pro:~ A$ 

[Ryan DeGroff]

Hi Ryan,

You should be able to run simulations from the GUI. What MacOS are you using?

Try removing the files in $HOME/Library/Application Support/SimVascular.

Cheers,
Dave

I am using Mac OS BigSur v11.4. I removed the files in that application support folder for SimVascular like you described, but when I try running the simulation I get the following error, almost as if the GUI is explicitly looking for a folder for open-mpi version 4.0.5, but my version is 4.1.1

Hi David, have you found a solution to this issue yet? I've tried uninstalling my current version 4.1.1 of open-mpi and installing version 4.0.5, but simulations continue to run unsuccessfully in the GUI.