[SOLVED] libtool: No such file or directory

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Javier_PalmaEspinosa
Posts: 12
Joined: Tue Nov 10, 2015 5:01 pm

[SOLVED] libtool: No such file or directory

Post by Javier_PalmaEspinosa » Tue Mar 01, 2016 9:49 am

Dear all,

Because of several issues with my computer, I had to install neuron all over again.
My computer runs last version of El Capitan. I followed the install walkthrough posted on https://www.neuron.yale.edu/neuron/down ... ilestd_osx
The installing process was smooth, except for the make install in nrn, which threw some error

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make[3]: Nothing to be done for `install-data-am'.
/Library/Developer/CommandLineTools/usr/bin/make  install-exec-hook
echo "enter install-exec-hook in nrn/Makefile.am"
enter install-exec-hook in nrn/Makefile.am
if test "--home=/Applications/NEURON-7.4/nrn" != "no" ; then \
		cd src/nrnpython ; \
		/usr/local/bin/python setup.py install --home=/Applications/NEURON-7.4/nrn ;\
	fi
running install
error: must supply either home or prefix/exec-prefix -- not both
make[3]: *** [install-exec-hook] Error 1
make[2]: *** [install-exec-am] Error 2
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1


I was able to solve this with the hint showed in viewtopic.php?f=4&t=2957
I run this

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Javier@Javiers-MacBook-Pro:~/Neuron/nrn$ cd src/nrnpython/
Javier@Javiers-MacBook-Pro:~/Neuron/nrn/src/nrnpython$ python setup.py install --prefix=/Applications/NEURON-7.4/nrn/lib
after that, I continued with the after install process

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Javier@Javiers-MacBook-Pro:~/neuron/nrn$ make after_install
carbon="" sh ./src/mac/after-install.sh "x86_64" "/Applications/NEURON-7.4/nrn" "." "/Applications/NEURON-7.4/iv/x86_64/lib"
folder bin of folder x86_64 of folder nrn of folder NEURON-7.4 of folder Applications of startup disk
Creating x86_64 directory for .o files.

/Applications/NEURON-7.4/nrn/share/nrn/demo/release
cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod
cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod
"/Applications/NEURON-7.4/nrn/x86_64/bin/nocmodl" cabpump
Translating cabpump.mod into cabpump.c
Notice: Assignment to the GLOBAL variable, "vol", is not thread safe
"/Applications/NEURON-7.4/nrn/share/nrn/libtool" --tag=CC --mode=compile gcc -DHAVE_CONFIG_H  -I. -I.. -I"/Applications/NEURON-7.4/nrn/include/nrn" -I"/Applications/NEURON-7.4/nrn/x86_64/lib"      -g -O2 -c -o cabpump.lo cabpump.c
/bin/sh: /Applications/NEURON-7.4/nrn/share/nrn/libtool: No such file or directory
make[1]: *** [cabpump.lo] Error 127
./neurondemo: line 27: /Applications/NEURON-7.4/nrn/share/nrn/demo/neuron: No such file or directory
./src/mac/after-install.sh: line 65: cd: .libs: No such file or directory
error: /Library/Developer/CommandLineTools/usr/bin/strip: can't open file: *.so (No such file or directory)
sed: neuron: No such file or directory
I am able to run nrngui, nrniv and use python module, i.e.

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from neuron import h
.

My main trouble stars when I try to compile mod scripts.

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Javier@Javiers-MacBook-Pro:~/neurociencia/Paper celula Granular/granular-cell-project/ver 2.0/Modelos/Palma-Espinosa$ nrnivmodl mod/
/Users/Javier/neurociencia/Paper celula Granular/granular-cell-project/ver 2.0/Modelos/Palma-Espinosa
mod//KIn.mod mod//NaSIn.mod mod//na8st.mod
KIn.mod NaSIn.mod na8st.mod
"/Applications/NEURON-7.4/nrn/share/nrn/libtool" --tag=CC --mode=compile gcc -DHAVE_CONFIG_H  -I. -I.. -I"/Applications/NEURON-7.4/nrn/include/nrn" -I"/Applications/NEURON-7.4/nrn/x86_64/lib"      -g -O2 -c -o KIn.lo `test -f 'KIn.c' || echo '/'`KIn.c
/bin/sh: /Applications/NEURON-7.4/nrn/share/nrn/libtool: No such file or directory
make: *** [KIn.lo] Error 127
Do you have any ideas?
Is there any more information that I may give in order to shed some light on this issue?

Thank you so much
Last edited by Javier_PalmaEspinosa on Wed Mar 02, 2016 4:22 pm, edited 1 time in total.

ted
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Re: libtool: No such file or directory

Post by ted » Tue Mar 01, 2016 12:05 pm


Javier_PalmaEspinosa
Posts: 12
Joined: Tue Nov 10, 2015 5:01 pm

Re: libtool: No such file or directory

Post by Javier_PalmaEspinosa » Tue Mar 01, 2016 1:34 pm

I've look the pdf.
As far as I understand, it says that I must install command line tools from XCode, which I have

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Javier@Javiers-MacBook-Pro:/Applications/NEURON-7.4/nrn/share/nrn$ which libtool
/usr/bin/libtool
what puzzles me is this line, when trying to compile a mod file

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/bin/sh: /Applications/NEURON-7.4/nrn/share/nrn/libtool: No such file or directory
make: *** [KIn.lo] Error 127
I don't get why there is no libtool in the folder.

Javier_PalmaEspinosa
Posts: 12
Joined: Tue Nov 10, 2015 5:01 pm

Re: libtool: No such file or directory

Post by Javier_PalmaEspinosa » Wed Mar 02, 2016 4:21 pm

I take it slowly this time. It was the lack of command tools, as you told in your link.
I uninstalled neuron, installed Command Tools, and reinstaled neuron. Now it works almost perfect (no mpi, but it is not critical).
Thank you!

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