Liggghts installation trouble - MPI_ABORT on running.

Submitted by bonnefoy on Wed, 08/22/2012 - 15:32

Hi everybody,

I am trying to install:

  • fftw-2.1.5.tar.gz
  • openmpi-1.4.5.tar.gz
  • liggghts-2.0.6 from git clone from LIGGGHTS-PUBLIC.git

The results are following:

  • The installation of FFTW went smoothly.
  • The installation of OPENMPI went smoothly too. A simple “hello_world” test gave results as expected, as well as the “mpirun” command.
  • The compilation of Liggghts went through without any major problem, except maybe the three lines at first:
    • grep: angle_*.h: No such file or directory
    • grep: dihedral_*.h: No such file or directory
    • grep: improper_*.h: No such file or directory
  • The execution of the executable with the “conveyor” example gave the following error message:

    ERROR on proc0: Cannot open log.liggghts (lammps.cpp:225)
    -------------------------------------------------------------------------------------
    MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1.
    NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.
    --------------------------------------------------------------------------------------

This error is motivating my demand for help. Can anybody suggest me any thing to make Liggghts work properly ?

Best regards, Olivier BONNEFOY

For debugging purposes, here are some other informations:

  • Before compilation, I added the two following lines at last in the /home/bonnefoy/.bashrc file:
    • export PATH=/home/bonnefoy/myopenmpi/files/bin:$PATH
    • export LD_LIBRARY_PATH=/home/bonnefoy/myopenmpi/files/lib:$LD_LIBRARY_PATH
  • After compilation, I added a symbolic link as:
    sudo ln -s /home/bonnefoy/myliggghts/src/lmp_myubuntu /usr/bin/liggghts
  • In order to fill in the MPI_INC, MPI_PATH and MPI_LIB in the Makefile, I successively typed:
    • mpicc –-showme:compile
    • mpicc –-showme:link
  • I also tried with openmpi-1.6 instead of openmpi-1.4.5. Same result.
  • FFTW.3.x seems not to be compatible with LIGGGHTS.
  • The Makefile used is:
    • # LIGGGHTS = Ubuntu 12.04, mpic++, openmpi-1.4.5, FFTW2
    • SHELL = /bin/bash
    • CC = /home/bonnefoy/myopenmpi/files/bin/mpic++
    • CCFLAGS = -g -O
    • DEPFLAGS = -M
    • LINK = /home/bonnefoy/myopenmpi/files/bin/mpic++
    • LINKFLAGS = -O
    • LIB = -lstdc++
    • ARCHIVE = ar
    • ARFLAGS = -rc
    • SIZE = size
    • LMP_INC = -DLAMMPS_GZIP
    • MPI_INC = -I/home/bonnefoy/myopenmpi/files/include
      -DMPICH_IGNORE_CXX_SEEK
    • MPI_PATH = -L/home/bonnefoy/myopenmpi/files/lib
    • MPI_LIB = -lmpi -lpthread -ldl -lm -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl
    • FFT_INC = -I/home/bonnefoy/myfftw/files/include -DFFT_FFTW
    • FFT_PATH = -L/home/bonnefoy/myfftw/files/lib
    • FFT_LIB = -lfftw

      •

Forums:

bonnefoy | Thu, 08/23/2012 - 00:24

Hello,

thank you for your idea. I found my mistake inbetween (see above).

Have a good evening too.

Olivier

Olivier Bonnefoy

msbentley's picture

msbentley | Wed, 08/22/2012 - 16:43

As a first sanity check, do you have write permissions wherever you are executing LIGGGHTS from? Generally I think the log file is written to the directory you are in when you execute the command, unless specified with the -log option.

Cheers, Mark

bonnefoy | Thu, 08/23/2012 - 00:23

Hi Mark,

Thanks for your suggestion. This was indeed the point. Everything went well afterwards and I could run and post-process and visualize the conveyor example with Paraview.

Have a good evening, Olivier

Olivier Bonnefoy

tianya4088 | Sun, 06/30/2013 - 08:50

Hi bonnefoy
I encounter with the same question, could you give a description of how to solve this problem in detail?
Have a nice day. Meng QX

Life-long Learning

bobsun | Tue, 02/05/2019 - 09:08

Dear CFDEM Programmer
I compiled CFDEM and LIGGGHTS together using command 'cfdemCompCFDEMall' and I encountered a similar problem when I tried to run an example named ErgunTestMPI_cgs. The error related to MPI_ABORT is merged as below.

MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

If you have some suggestions for me to solve this problem, please provide some comments. Thank you very much.

Best regards,
Bob