Configuring and Compiling External Packages

Chaco Multilevel Graph Partitioning Tool

Error compiling on macOS

When compiling Chaco on macOS (most likely using the ${ISSM_DIR}/externalpackages/chaco/install.sh script), you may encounter an error that reads,

util/smalloc.c:6:10: fatal error: 'malloc.h' file not found
#include <malloc.h>
         ^~~~~~~~~~
1 error generated.
make: *** [util/smalloc.o] Error 1

To correct this, you will have to have either Xcode Command Line Tools (preferred) or Xcode installed:

To install the Xcode Command Line Tools, run xcode-select --install
You can install Xcode through the Mac App Store

You will then need to modify the CPATH environment variable in your shell profile (e.g. ~/.bashrc),

If you installed the Xcode Command Line Tools,

export CPATH="/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/malloc:/usr/include"

If you installed Xcode,

export CPATH="/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/malloc:/usr/include"

Then, source your shell profile again and rerun the installation script.

PETSc

Timeout: Unable to run MPI program

When downloading MPICH via PETSc, you may encounter an error after the configuration and make stages that reads something like,

=============================================================================================
  Trying to download
  https://github.com/pmodels/mpich/releases/download/v5.0.0/mpich-5.0.0.tar.gz for MPICH
=============================================================================================
=============================================================================================
                  Running configure on MPICH; this may take several minutes
=============================================================================================
=============================================================================================
                     Running make on MPICH; this may take several minutes
=============================================================================================
=============================================================================================
                 Running make install on MPICH; this may take several minutes
=============================================================================================
TESTING: configureMPIEXEC from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:201)
*********************************************************************************************
           UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
---------------------------------------------------------------------------------------------
  Timeout: Unable to run MPI program with
  <ISSM_DIR>/externalpackages/petsc/install/bin/mpiexec -n 1
  (1) make sure this is the correct program to run MPI jobs
  (2) your network may be misconfigured; see
  https://petsc.org/release/faq/#mpi-network-misconfigure
  (3) you may have VPN running whose network settings may not play nice with MPI
********************************************************************************************

The PETSc FAQ page indicates that it may be a missing entry in the /etc/hosts file. However, if the issue persists, run export HWLOC_COMPONENTS=stop (or add it to the PETSc installation script before the configure step) and then rerun the PETSc installation script. If this fixes the issue where MPI hangs, add the following to your shell profile (e.g. ~/.bash_profile) to create a persistent fix for MPICH,

export HWLOC_COMPONENTS=stop

Error running make on <EXT_PKG>

When using PETSc to install an external package you may encounter a failure that reads,

Error running make on <EXT_PKG>

Inspection of src/configure.log should reveal a line similar to,

Error running make on <EXT_PKG>: Could not execute "['<CMD_STRING>']":

This is usually not a very helpful error message. What you can do is copy <CMD_STRING> and run it manually on the command line to reveal and correct the underlying errors.

Error running configure on MPICH

With GCC 10 and later, when using PETSc to install MPICH, you may encounter a failure that reads,

Error running configure on MPICH

Inspection of src/configure.log should reveal,

error: The Fortran compiler gfortran will not compile files that call
the same routine with arguments of different types.

One way to get around this is to add,

--FFLAGS="-fallow-argument-mismatch"

to the list of configuration arguments.

C++ error! MPI_Finalize() could not be located! / Error running make; make install on MPICH

When configuring and/or compiling MPICH via PETSc, it may fail with either of the above error messages. Inspection of src/configure.log should reveal something like,

Checking for program /opt/homebrew/bin/mpicc...found

The solution here is one of the following:

Uninstall the MPI compiler set installed via package manager (in this example, Homebrew)
Make sure that the path to the desired non-MPI compiler set (e.g. gcc, g++) appears in the PATH environment variable before the path to the offending MPI compiler set
Remove the --download-mpich=1 option from the PETSc configuration and instead supply the appropriate options to use the alternate MPI implementation