petsc compilation

dalcome

Hi all,
I'm trying to install ISSM and the compilation stopped while installing petsc.

TESTING: configureMPIEXEC from config.packages.MPI(/home/shkim/software/issm/trunk/externalpackages/petsc/src/config/BuildSystem/config/packages/MPI.py)

the compilation stops at this stage. I've already installed mpich and cmake. Does anybody know what the problem is?

Thanks in advance.

mathieumorlighem

Hi,
most likely your installation of mpich did not work or you cannot run mpiexec. Can you try and compile the following program (call it test.cpp):

#include <iostream>
int main(){
	std: << "hello world!\n";
	return 0;
}

compile it like this:

g++ test.cpp

and then run

mpiexec -np 3 ./a.out

You should see 3 times "Hello World!". If you don't let us know what you get.
Mathieu

dalcome

Hi,
I ran the command line after revising it to :

mpiexec -np 3 -host localhost ./a.out

Then, I got 3 hello world!
Thanks,

========================================================================
additional info:

i compiled mpich with

./configure \
        --prefix="$ISSM_DIR/externalpackages/mpich/install" \
        --enable-shared \
        --enable-sharedlibs=gcc \
        --with-pm=gforker

then, petsc installation was done without any problem. But now, when I do make install ISSM, I'm getting a lot of this warning:

libtool: relink: warning: 'issm/trunk/externalpackages/mpich/install/lib//libmpich.la' seems to be moved

mathieumorlighem

Hi,
make sure to run this before you make:

cd $ISSM_DIR
autoreconf -iv
./configure.sh

make sure that each of these commands return without an error. Let us know if the error persists.

Mathieu

dalcome

Hi,
when I do ./configure , I don't get any error msg,
then when I make, I get these errors:

./classes/IoModel.cpp: In member function 'void IoModel:(IssmDouble**, int*, int*, const char*)':
./classes/IoModel.cpp: error: 'uint8_t' was not declared in this scope
./classes/IoModel.cpp: error: 'rawmatrix' was not declared in this scope
./classes/IoModel.cpp: error: 'uint8_t' cannot appear in a constant-expression
./classes/IoModel.cpp: error: no matching function for call to 'xNew(int)'
./classes/IoModel.cpp: error: 'uint8_t' cannot appear in a constant-expression

So, I tried to do make with these configuration settings:

./configure \
        --prefix=$ISSM_DIR \
        --with-matlab-dir="$ISSM_DIR/externalpackages/matlab/install" \
        --with-triangle-dir="$ISSM_DIR/externalpackages/triangle/install" \
        --with-mpi-include="$ISSM_DIR/externalpackages/mpich/install/include" \
        --with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib/ -lmpich" \
        --with-petsc-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-metis-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-blas-lapack-dir="$ISSM_DIR/externalpackages/petsc/install" \
        --with-scalapack-dir="$ISSM_DIR/externalpackages/petsc/install/" \
        --with-mumps-dir="$ISSM_DIR/externalpackages/petsc/install/" \
        --with-m1qn3-dir="$ISSM_DIR/externalpackages/m1qn3/install" \
        --with-numthreads=24

Then, make gives two types of Warnings,

*** Warning: Linking the shared library libISSMCore.la against the
*** static library /home/shkim/software/issm/trunk/externalpackages/m1qn3/install/libm1qn3.a is not portable!

*** Warning: Linking the shared library libISSMCore.la against the
*** static library /home/shkim/software/issm/trunk/externalpackages/m1qn3/install//libddot.a is not portable!

*** Warning: Linking the shared library libISSMModules.la against the
*** static library /home/shkim/software/issm/trunk/externalpackages/triangle/install/triangle.a is not portable!

*** Warning: Linking the shared library M1qn3_matlab.la against the
*** static library /home/shkim/software/issm/trunk/externalpackages/m1qn3/install/libm1qn3.a is not portable!

*** Warning: Linking the shared library M1qn3_matlab.la against the
*** static library /home/shkim/software/issm/trunk/externalpackages/m1qn3/install//libddot.a is not portable!

*** Warning: Linking the shared library TriMesh_matlab.la against the
*** static library /home/shkim/software/issm/trunk/externalpackages/triangle/install/triangle.a is not portable!

and

libtool: link: warning: '/home/shkim/software/issm/trunk/externalpackages/mpich/install/lib//libmpich.la' seems to be moved

mathieumorlighem

Yeah you should not call configure like that, but provide options as you did the second time. You can ignore the warnings, I am a bit worried about the libmpich.la warning, but maybe it did work. Try to run issmversion in MATLAB (https://issm.jpl.nasa.gov/documentation/addpath/) and you will see if it worked or not.

Mathieu

dalcome

Mathieu,
I get the messages below when I do issmversion:

Ice Sheet System Model (ISSM) Version 4.12
(website: http://issm.jpl.nasa.gov contact: issm@jpl.nasa.gov)

Build date: Tue Dec 12 01 KST 2017
Compiled on unknown linux x86_64 by shkim

Copyright (c) 2009-2017 California Institute of Technology

    to get started type: issmdoc

Then, I tried to run runme as in examples. The below is what I got:

runme
      creating thickness
      creating drag
      initial velocity
      creating flow law parameter
      creating boundary conditions
      boundary conditions for stressbalance model: spc set as zero
      no smb.mass_balance specified: values set as zero
      no basalforcings.groundedice_melting_rate specified: values set as zero
      no basalforcings.floatingice_melting_rate specified: values set as zero
      no balancethickness.thickening_rate specified: values set as zero
      no thermal boundary conditions created: no observed temperature found
checking model consistency
marshalling file Square.bin
uploading input file and queueing script
launching solution sequence on remote cluster
mpiexec failed: gethostbyname_ex failed for Sentinel
source /home/shkim/software/issm/trunk//etc/environment.sh && cd /home/shkim/software/issm/trunk//execution && rm -rf ./Square-12-12-2017-13-03-24-4426 && mkdir Square-12-12-2017-13-03-24-4426 && cd Square-12-12-2017-13-03-24-4426 && mv ../Square-12-12-2017-13-03-24-4426.tar.gz ./ && tar -zxf Square-12-12-2017-13-03-24-4426.tar.gz  && source  Square.queue : Signal 127
loading results from cluster
Error using loadresultsfromdisk (line 17)

============================================================
   Binary file Square.outbin not found

   This typically happens when the run crashed.
   Please check for error messages above or in the outlog
============================================================

Error in loadresultsfromcluster (line 30)
md=loadresultsfromdisk(md,);

Error in solve (line 165)
        md=loadresultsfromcluster(md);

Error in runme (line 7)
md=solve(md,'Stressbalance');

mathieumorlighem

Hi,
yes, it has been the same problem all along. You are probably using vpn or a weird wifi, and MPI does not know your computer name. Could you try the following https://issm.ess.uci.edu/flarum/d/82-ssh-could-not-resolve-hostname and add your computer name (from MATLAB you can do oshostname() to get it) to /etc/hosts and see if it works?

Mathieu

dalcome

Hi Mathieu,
I followed the link you provided and added the name to /etc/hosts. Still did not work.
So I started re-installing everything again and guess what, it works now.
I was able to run the Square example.

Thank you, :

mattiapoinelli

hello there,
trying to install petsc after I installed mpich and cmake.
Here the problem:

===============================================================================

             Configuring PETSc to compile on your system                       

===============================================================================

===============================================================================                                                     

  ***** WARNING: MPI_DIR (set to /Users/poinelli/Documents/ISSM/trunk/externalpackages/mpich/install) found in environment v    

     use ./configure MPI_DIR=$MPI_DIR if you really want to use that value ******                                             
     ===============================================================================                                                 
     ===============================================================================                                                               
    
    WARNING! Compiling PETSc with no debugging, this should                                                                       
            only be done for timing and production runs. All development should                                                  
                       be done when configured using --with-debugging=1                                                          
                       ===============================================================================                                               
     
      TESTING: checkCLibraries from config.compilers(config/BuildSystem/config/compilers.py)                                      
      *******************************************************************************
      
         UNABLE to CONFIGURE with GIVEN OPTIONS    (see configure.log for details):

-------------------------------------------------------------------------------

C libraries cannot directly be used from Fortran

*******************************************************************************

So I tried to follow Mathieu indication for the 3time Hello World test and it didn't work showing this:

ssh: Could not resolve hostname lmc-065524: nodename nor servname provided, or not known

Many thanks for the help!