Problem installing on cluster

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jtg374
Posts: 3
Joined: Tue Jun 25, 2019 5:55 am

Problem installing on cluster

Post by jtg374 » Tue Jun 25, 2019 11:17 pm

Hi everyone,
I am trying installation on a cluster following this post. With the advice of the administrator, I created a conda virtual environment with all possible dependencies I can find.

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module load anaconda3/5.2.0
module load openmpi/gnu.3.1.3
conda create -n NEURON -c conda-forge python=3.4
Then I downloaded nrn 7.6 and followed the installation script:

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#!/bin/sh
../nrn/configure --prefix=`pwd` --with-nmodl-only --without-x
make
make install

../nrn/configure --prefix=`pwd` '--without-nmodl' '--without-x' \
'--without-memacs' '--with-paranrn' 'CC=mpicc' 'CXX=mpicxx' \
'--disable-shared' 'CFLAGS=-g -O0' 'CXXFLAGS=-g -O0'  linux_nrnmech=no
make
make install

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tar xzf nrn-7.6.tar.gz
mv nrn-7.6 nrn
mkdir mpi
cd mpi
sh ../nrninstall.sh &> installnotes.log
The compilation with-nmodl-only succeeded but the nrniv compilation encoutered MAKE ERROR:

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......
......
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/gpfsnyu/home/jtg374/neuron/mpi3/src/parallel'
make[2]: Leaving directory '/gpfsnyu/home/jtg374/neuron/mpi3/src/parallel'
Making install in nrniv
make[2]: Entering directory '/gpfsnyu/home/jtg374/neuron/mpi3/src/nrniv'
/bin/sh ../../libtool  --tag=CXX   --mode=link mpic++  -g -O0   -o nrniv nvkludge.o ../ivoc/nrnmain.o ../ivoc/ivocmain.o ../oc/modlreg.o ../oc/ockludge.o ../nrnoc/libnrnoc.la ../oc/liboc.la libnrniv.la ../ivoc/libivoc.la ../oc/liboc.la ../nrnmpi/libnrnmpi.la     ../gnu/libneuron_gnu.la ../scopmath/libscopmath.la ../sparse13/libsparse13.la ../sundials/libsundials.la ../mesch/libmeschach.la ../ivos/libivos.la    -lm -ldl
libtool: link: mpic++ -g -O0 -o nrniv nvkludge.o ../ivoc/nrnmain.o ../ivoc/ivocmain.o ../oc/modlreg.o ../oc/ockludge.o  ../nrnoc/.libs/libnrnoc.a ./.libs/libnrniv.a ../ivoc/.libs/libivoc.a ../oc/.libs/liboc.a ../nrnmpi/.libs/libnrnmpi.a ../gnu/.libs/libneuron_gnu.a ../scopmath/.libs/libscopmath.a ../sparse13/.libs/libsparse13.a ../sundials/.libs/libsundials.a ../mesch/.libs/libmeschach.a ../ivos/.libs/libivos.a /gpfsnyu/packages/openmpi/gnu/3.1.3/lib/libmpi.so /gpfsnyu/packages/openmpi/gnu/3.1.3/lib/libopen-rte.so /gpfsnyu/packages/openmpi/gnu/3.1.3/lib/libopen-pal.so -lrt -lutil -lz -lm -ldl -pthread -Wl,-rpath -Wl,/gpfsnyu/packages/openmpi/gnu/3.1.3/lib -Wl,-rpath -Wl,/gpfsnyu/packages/openmpi/gnu/3.1.3/lib
./.libs/libnrniv.a(bbsrcli.o): In function `BBSClient::done()':
/gpfsnyu/home/jtg374/neuron/mpi3/src/nrniv/../../../nrn/src/nrniv/../parallel/bbsclimpi.cpp:317: undefined reference to `p_nrnpython_finalize'
./.libs/libnrniv.a(bbsrcli.o): In function `BBSClient::done()':
bbsrcli.cpp:(.text+0xafd): undefined reference to `p_nrnpython_finalize'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:746: nrniv] Error 1
make[2]: Leaving directory '/gpfsnyu/home/jtg374/neuron/mpi3/src/nrniv'
make[1]: *** [Makefile:517: install-recursive] Error 1
make[1]: Leaving directory '/gpfsnyu/home/jtg374/neuron/mpi3/src'
make: *** [Makefile:654: install-recursive] Error 1

Can you help? thanks!

jtg374
Posts: 3
Joined: Tue Jun 25, 2019 5:55 am

Re: Problem installing on cluster

Post by jtg374 » Wed Jun 26, 2019 9:38 pm

Hi,
The cluster administrator helped installation in the public folder. There is no further problems. Thanks!

--
Yes, what I do is get it installed from source.



Step 1. download the two packages iv and nrn
Step 2. install iv. For I am root, then I could get it installed in a public folder. If you like make it, let it goes to your home folder.
Step 3. install iv
tar xvf iv.***.gz
cd iv
./configure --prefix=/where to install
make
make install

Configure the environment of them
export PATH=...(where to find the bin):$PATH
export CPATH=...(where to find the include) :$CPATH
export LD_LIBRARY_PATH=...(where to find the lib):$LD_LIBRARY_PATH


Step 4. install nrn
module load iv/19 anaconda3/5.2.0
tar xvf nrn.***.gz
cd nrn
./configure --prefix=/where to install --with-iv --with-nrnpython --with-paranrn
make
make install
cd src/nrnpython
python setup.py install

Configure the environment of them
export PATH=... :$PATH
export CPATH=... : $CPATH
export LD_LIBRARY_PATH=... :$LD_LIBRARY_PATH
export PYTHONPATH=.... :$PYTHONPATH

In cluster, we use module to manage the environment variables (PATH, CPATH ..), The file you can find at /gpfsnyu/modules/iv/19 and /gpfsnyu/modules/nrn/7.6


In case, if there are some error generated during your computing, please let me know.

ted
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Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Problem installing on cluster

Post by ted » Thu Jun 27, 2019 10:29 am

Thank you for providing the solution to your problem!

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