allow MPI compiler to be set with CXX=... instead of MPICXX=...

[kitchenknif]

Using the build steps from the build script found the docs (http://meep.readthedocs.io/en/latest/Build_From_Source/),

cd ~/install
git clone https://github.com/stevengj/meep.git
cd meep/
sh autogen.sh --enable-shared --with-mpi PYTHON=python3 \
    CC=mpicc CXX=mpic++ LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make && sudo make install

On CentOS 6.9, with a custom built OpenMPI, installed to /usr/local and a custom built HDF5, also in /usr/local, the link commands executed during sudo make install fall over because they are unable to find mpic++.
LDFLAGS, CC, CXX, CPPFLAGS are all modified to point to the correct directories.
CC and CXX point to the full paths of mpicc/mpic++, e.g. CXX=/usr/local/bin/mpic++.
Running make install from root works correctly, /usr/local/bin is in the system path.
Passing the environment variable to sudo with sudo -E doesn't help...

This is the exact command that falls over:

libtool: install: warning: relinking `libmeepgeom.la'
libtool: install: (cd /home/pdmitriev/install/meep/libmeepgeom; /bin/sh /home/pdmitriev/install/meep/libtool  --silent --tag CXX --mode=relink mpic++ -O3 -fstrict-aliasing -mtune=native -Wall -W -version-info 10:0:0 -L/usr/local/lib -L/usr/local/lib/openmpi -Wl,-rpath,/usr/local/lib:/usr/local/lib/openmpi -o libmeepgeom.la -rpath /usr/local/lib meepgeom.lo GDSIIgeom.lo ../src/libmeep.la -lhdf5 -lz -lgsl -lgslcblas -lm -lmpb -L/usr/local/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lharminv -llapack -lblas -lgfortranbegin -lgfortran -lm -llapack -lblas -lfftw3 -lm -L/usr/local/lib -L/usr/local/lib/openmpi -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.. -lfftw3 -lgfortranbegin -lgfortran -lm )
/home/pdmitriev/install/meep/libtool: line 7841: mpic++: command not found
libtool: install: error: relink `libmeepgeom.la' with the above command before installing it

Not sure if this is me having screwed up my setup or a bug in the makefiles...

[stevengj]

If mpic++ is not in your path, then you should either add /usr/local/bin to your PATH environment variable or specify the full path in CXX=/usr/local/bin/mpic++. See http://meep.readthedocs.io/en/latest/Build_From_Source/#installation-paths

[acmcclung]

I have this problem too, despite mpic++ being in my path. I have gotten around it by manually editing libtool to the full path after getting the error (in my case on CentOS by changing CC="mpic++" to CC="/usr/lib64/openmpi/bin/mpic++") and calling sudo make install again.

Specifying the full path for autogen.sh on the command line strangely does not solve the problem, as the generated libtool file does not have the specified path.

[kitchenknif]

That's the problem -
mpic++ is in the PATH and i've specified the full path to mpic++, CXX=/usr/local/bin/mpic++
and sudo -E make install still fails to find mpic++

[kitchenknif]

This is the required modification to correctly make meep:

export RPATH_FLAGS="-Wl,-rpath,/usr/local/lib:/usr/local/lib/openmpi"
export MY_LDFLAGS="-L/usr/local/lib -L/usr/local/lib/openmpi ${RPATH_FLAGS}"
export MY_CPPFLAGS="-I/usr/local/include -I/usr/local/include/openmpi"

mkdir ~/install
cd ~/install
git clone https://github.com/stevengj/meep.git
cd meep/
sh autogen.sh --enable-shared --with-mpi PYTHON=python3 CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpic++ LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make -j
sed -i 's/CC="mpic++"/CC="\/usr\/local\/bin\/mpic++"/g' libtool
sudo make install

[stevengj]

I'm guessing that the mpic++ in your PATH is not the same as /usr/local/bin/mpicc (i.e. you have two versions of MPI installed) … what does which mpic++ report at the shell prompt?

For --with-mpi, you have to set MPICXX=/usr/local/bin/mpic++, as otherwise it looks for mpic++ in your path first.

(I guess the ACX_MPI script could be updated to first check whether CXX is already an MPI compiler before looking for mpic++...)

[kitchenknif]

No, I have only one mpic++ installed, the one that is in /usr/local/bin/ But /usr/local/bin isn't in PATH by default, I add it through an equivalent of .bashrc, meaning the it is not in the PATH that sudo sees. Funnily enough though, sudo -E, which should preserve environment vars, still doesn't see mpic++...

…

On Thu, Jun 14, 2018, 20:50 Steven G. Johnson ***@***.***> wrote: I'm guessing that the mpic++ in your PATH is not the same as /usr/local/bin/mpicc (i.e. you have two versions of MPI installed) … what does which mpic++ report? For --with-mpi, you have to set MPICXX=/usr/local/bin/mpic++. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#379 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AH2oYQ41K72RcyCzgcrMWo6LTdIzjof8ks5t8lwfgaJpZM4Uj4T_> .

[stevengj]

You shouldn’t run configure with sudo, generally. Only use sudo for the final make install step (after configure and make). The general principle is to do as little as possible with root privileges.

[kitchenknif]

Passing mpicc, mpic++ as MPICC and MPICXX works, yes.

[kitchenknif]

This script successfully builds meep on a clean CentOS 6 install.
Though I probably makes sense to break it up...
Building swig and Guile may not be necessary, though I remember having problems with the ones that came with CentOS 6

I build OpenMPI, HDF5 and Python3 because the versions that come with CentOS 6 are hopelessly out of date.

#!/bin/bash

set -e

RPATH_FLAGS="-Wl,-rpath,/usr/local/lib:/usr/local/lib/openmpi"
MY_LDFLAGS="-L/usr/local/lib -L/usr/local/lib/openmpi ${RPATH_FLAGS}"
MY_CPPFLAGS="-I/usr/local/include -I/usr/local/include/openmpi"

#
# yum installs
#
sudo yum -y --enablerepo=extras install epel-release
sudo yum -y install bison byacc cscope ctags cvs diffstat doxygen flex gcc gcc-c++ gcc-gfortran gettext git indent intltool libtool patch patchutils rcs redhat-rpm-config rpm-build subversion systemtap wget
sudo yum -y install openblas-devel fftw3-devel libpng-devel gsl-devel gmp-devel pcre-devel libtool-ltdl-devel libunistring-devel libffi-devel gc-devel zlib-devel openssl-devel sqlite-devel bzip2-devel

#
# time to build
#
sudo rm -rf ~/install
mkdir -p ~/install


cd ~/install
wget https://github.com/swig/swig/archive/rel-3.0.12.tar.gz
tar xvf rel-3.0.12.tar.gz
cd swig-rel-3.0.12
./autogen.sh
./configure
make -j
sudo make -j install


cd ~/install
wget https://ftp.gnu.org/gnu/guile/guile-2.0.11.tar.gz
tar xvf guile-2.0.11.tar.gz
cd guile-2.0.11
./configure
make -j
sudo make -j install


cd ~/install
wget https://www.python.org/ftp/python/3.6.5/Python-3.6.5.tgz
tar xvf Python-3.6.5.tgz
cd Python-3.6.5
./configure --enable-optimizations
make -j
sudo make -j install


cd ~/install
wget https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.1.tar.gz
tar xvf openmpi-2.1.1.tar.gz
cd openmpi-2.1.1/
./configure
make -j all
sudo make -j install


cd ~/install
git clone https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git
cd hdf5/
git checkout tags/hdf5-1_10_2
./configure --enable-parallel --enable-shared --prefix=/usr/local CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpic++
make -j
sudo make -j install


cd ~/install
git clone https://github.com/stevengj/harminv.git
cd harminv/
sh autogen.sh --enable-shared
make -j
sudo make -j install


cd ~/install
git clone https://github.com/stevengj/libctl.git
cd libctl/
sh autogen.sh  --enable-shared
make -j
sudo make -j install


cd ~/install
git clone https://github.com/stevengj/h5utils.git
cd h5utils/
sh autogen.sh CC=/usr/local/bin/mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make -j
sudo make -j install

cd ~/install
git clone https://github.com/stevengj/mpb.git
cd mpb/
sh autogen.sh --enable-shared CC=/usr/local/bin/mpicc LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}" --with-hermitian-eps
make -j
sudo make -j install


cd ~/install
wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-3.0.0.tar.gz
tar xvf mpi4py-3.0.0.tar.gz
cd mpi4py-3.0.0/
python3 setup.py build
sudo /usr/local/bin/python3 setup.py install


cd ~/install
wget https://github.com/h5py/h5py/archive/2.8.0.tar.gz
tar xvf 2.8.0.tar.gz
cd h5py-2.8.0/
python3 setup.py configure --mpi
python3 setup.py build
sudo /usr/local/bin/python3 setup.py install


cd ~/install
git clone https://github.com/stevengj/meep.git
cd meep/
sh autogen.sh --enable-shared --with-mpi PYTHON=python3 MPICC=/usr/local/bin/mpicc MPICXX=/usr/local/bin/mpic++ LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
#sh autogen.sh --enable-shared --with-mpi PYTHON=python3 CC=/usr/local/bin/mpicc CXX=/usr/local/bin/mpic++ LDFLAGS="${MY_LDFLAGS}" CPPFLAGS="${MY_CPPFLAGS}"
make -j
#sed -i 's/CC="mpic++"/CC="\/usr\/local\/bin\/mpic++"/g' libtool
sudo make install

And another issue - this builds a python wrapper that cannot be imported without appyling the patch

--- __init__.py	2018-06-15 20:15:11.062122018 +0800
+++ __init__.py_new	2018-06-15 20:15:48.622122038 +0800
@@ -8,7 +8,8 @@
 if _swig_python_version_info >= (2, 7, 0):
     def swig_import_helper():
         import importlib
-        pkg = __name__.rpartition('.')[0]
+        pkg_parts = __name__.rpartition('.')
+        pkg = pkg_parts[0] if pkg_parts[1] == '.' else pkg_parts[2]
         mname = '.'.join((pkg, '_meep')).lstrip('.')
         try:
             return importlib.import_module(mname)
@@ -4467,5 +4468,3 @@
 atexit.register(report_elapsed_time)
 
 # This file is compatible with both classic and new-style classes.
-
-

by
sudo patch /usr/local/lib/python3.6/site-packages/meep/__init__.py < import.patch

[stevengj]

For the swig patch, see #189. There is a bug for SWIG 3.0.[9,10,11,12] and currently we only work around the problem for 3.0.12. Updates for other SWIG versions would be welcome.

(Hmm, it looks like you are using SWIG 3.0.12, though, which should already be handled by a patch in our Makefile?)

[stevengj]

Note that 5ba3b72 fixes the documentation problem in the original post: setting CXX=... in the --with-mpi Ubuntu build instructions was not actually doing anything, nor was it needed.

[stevengj]

Note that to allow the MPI compiler to be set with CXX=..., the right way would be to modify https://github.com/NanoComp/meep/blob/master/m4/acx_mpi.m4 so that it first checks whether $CXX works for linking/compiling MPI code, and only afterwards try $MPICXX.