error message: nrnmpi_dynam.h: No such file or directory

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ibuki
Posts: 9
Joined: Wed Mar 26, 2014 5:33 am

error message: nrnmpi_dynam.h: No such file or directory

Post by ibuki » Thu Apr 03, 2014 10:12 pm

Hello everyone,

I'm trying to install the newest version of NEURON on my osx 10.7 with openmpi. Everything seemed fine to me until I ran into this:

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Making all in nrnmpi
/bin/sh ../../libtool  --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/oc  -I.    -g -O2 -MT nrnmpi.lo -MD -MP -MF .deps/nrnmpi.Tpo -c -o nrnmpi.lo nrnmpi.c
libtool: compile:  mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/oc -I. -g -O2 -MT nrnmpi.lo -MD -MP -MF .deps/nrnmpi.Tpo -c nrnmpi.c  -fno-common -DPIC -o .libs/nrnmpi.o
nrnmpi.c:10:79: error: nrnmpi_dynam.h: No such file or directory
make[3]: *** [nrnmpi.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
host-002:nrn ibuki$ sudo makePassword:
make  all-recursive
Making all in src
Making all in memacs
make[3]: Nothing to be done for `all'.
Making all in e_editor
make[3]: Nothing to be done for `all'.
Making all in modlunit
make[3]: Nothing to be done for `all'.
Making all in nmodl
make[3]: Nothing to be done for `all'.
Making all in sparse
make[3]: Nothing to be done for `all'.
Making all in sparse13
make[3]: Nothing to be done for `all'.
Making all in scopmath
make[3]: Nothing to be done for `all'.
Making all in Random123
make[3]: Nothing to be done for `all'.
Making all in nrnmpi
/bin/sh ../../libtool  --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/oc  -I.    -g -O2 -MT nrnmpi.lo -MD -MP -MF .deps/nrnmpi.Tpo -c -o nrnmpi.lo nrnmpi.c
libtool: compile:  mpicc -DHAVE_CONFIG_H -I. -I../.. -I../../src/nrnoc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/oc -I. -g -O2 -MT nrnmpi.lo -MD -MP -MF .deps/nrnmpi.Tpo -c nrnmpi.c  -fno-common -DPIC -o .libs/nrnmpi.o
nrnmpi.c:10:79: error: nrnmpi_dynam.h: No such file or directory
make[3]: *** [nrnmpi.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
I followed the instructions on this page: http://www.neuron.yale.edu/neuron/downl ... ilestd_osx
and I was at step "D. Install NEURON" under the second section (II. Installing InterViews and NEURON.) The error messages appeared after I use the "make".

Thank you for your attention and I appreciate your help in advance!
Last edited by ibuki on Fri Apr 04, 2014 8:14 am, edited 1 time in total.

hines
Site Admin
Posts: 1492
Joined: Wed May 18, 2005 3:32 pm

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by hines » Fri Apr 04, 2014 7:04 am

I need to fix a make dependency problem when the configure option --with-paranrn=dynamic is used. To work around the problem
cd nrn/src/nrnmpi
sh mkdynam.sh
Then you can go back to the top level build folder and type 'make ; make install ; make after_install'

ibuki
Posts: 9
Joined: Wed Mar 26, 2014 5:33 am

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by ibuki » Fri Apr 04, 2014 8:14 am

Thank you! This works perfectly fine.

However, when I was trying to do the test run, it gives an error message like this:

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Ibukis-MacBook-Pro:parallel ibuki$ mpirun -n 4 $N/$CPU/bin/nrniv -mpi test0.hoc
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not access
or execute an executable:

Executable: //bin/nrniv
Node: Ibukis-MacBook-Pro

while attempting to start process rank 0.
--------------------------------------------------------------------------
4 total processes failed to start
I'm sorry if this question sounds way too silly.

Thanks again!

Ibuki

ted
Site Admin
Posts: 5213
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by ted » Fri Apr 04, 2014 2:24 pm

A path problem; step "E" should have taken care of that. Did you create a nrnenv in $HOME/neuron/ with these contents?

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export IV=$IDIR/
export N=$IDIR/nrn
export CPU=x86_64
export PATH=$IV/$CPU/bin:$N/$CPU/bin:$PATH
What happens when you execute
echo $N
or
echo $CPU
?
Where is nrniv actually located?

ibuki
Posts: 9
Joined: Wed Mar 26, 2014 5:33 am

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by ibuki » Sat Apr 05, 2014 8:10 am

Hello Ted,

1. Yes, I have a file like that named "nrnenv", which includes the content:

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export IV=$IDIR/iv
export N=$IDIR/nrn
export CPU=x86_64
export PATH=$IV/$CPU/bin:$N/$CPU/bin:$PATH

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ibukis-MacBook-Pro:neuron ibuki$ ls
iv	nrn	nrnenv
I'm sorry, but should the

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export IV=$IDIR/
be

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export IV=$IDIR/iv
?

2.

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ibukis-MacBook-Pro:neuron ibuki$ echo $N
/nrn
ibukis-MacBook-Pro:neuron ibuki$ echo $CPU
x86_64
3.

Code: Select all

/Users/ibuki/neuron/nrn/src/nrniv 
Please let me know if you have any further questions, thank you!

ted
Site Admin
Posts: 5213
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by ted » Sat Apr 05, 2014 1:46 pm

Does NEURON start if you execute this command:
/Users/ibuki/neuron/nrn/src/nrniv
?

ibuki
Posts: 9
Joined: Wed Mar 26, 2014 5:33 am

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by ibuki » Sat Apr 05, 2014 3:00 pm

No, I don't think it works:

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ibukis-MacBook-Pro:~ ibuki$ /Users/ibuki/neuron/nrn/src/nrniv
-bash: /Users/ibuki/neuron/nrn/src/nrniv: is a directory

hines
Site Admin
Posts: 1492
Joined: Wed May 18, 2005 3:32 pm

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by hines » Sun Apr 06, 2014 2:43 pm

What is the value of $IDIR ? For the 7.3 version on the mac I generally use (bash shell)
export IDIR=/Applications/NEURON-7.3
Anyway, the installed executables would be in $IDIR/nrn/x86_64/bin so in a terminal you should be able to run
/Applications/NEURON-7.3/nrn/x86_64/bin/nrniv
Note that $IDIR/nrn is what you presumably used for configure's --prefix .

ibuki
Posts: 9
Joined: Wed Mar 26, 2014 5:33 am

Re: error message: nrnmpi_dynam.h: No such file or directory

Post by ibuki » Mon Apr 07, 2014 8:01 am

Code: Select all

ibukis-MacBook-Pro:~ ibuki$ /Applications/NEURON-7.3/nrn/x86_64/bin/nrniv
NEURON -- Release 7.3 (1059:24c7ee8666e7) 24c7ee8666e7
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2014
See http://www.neuron.yale.edu/neuron/credits

oc>
Yes, this command seems to work.

Any further comments on how to make the mpi stuff work?

Thank you!

ibuki

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