NEURON can't find IV headers/libs

Post Reply
phendric
Posts: 18
Joined: Tue Apr 21, 2009 12:57 am

NEURON can't find IV headers/libs

Post by phendric »

Hi all,

I'm currently compiling NEURON to run on a CentOS-based cluster we recently set up. I followed the instructions to compile InterViews, which completed successfully. However, when I try to run ./configure on the NEURON source files, I eventually get the error:
...
checking compilation with interviews... failed
I can't compile and/or link an interviews program. If InterViews is not
installed in /usr or /usr/local or /usr/local/iv,
specify the proper location of the interviews tree using

configure --with-iv=/where/you/put/iv

The interviews headers should be in subdirectories of
/where/you/put/iv/include, and the libraries should be in
/where/you/put/iv/lib or /where/you/put/iv/x86_64/lib
(not in /where/you/put/iv/lib/ALPHA or
/where/you/put/iv/lib/LINUX or some other subdirectory of lib).

If you don't want interviews, but do want nrniv built with the non-gui
c++ classes then specify configure --without-iv.
However, both the IV libraries and headers exist, as shown by the following:

Code: Select all

[phendric@hpc-login2 iv]$ pwd
/auto/rcf-proj3/tb/phendric/nrn70/iv

[phendric@hpc-login2 iv]$ ls
acinclude.m4  config.guess   config.sub    INSTALL     makedist       README
aclocal.m4    config.h       configure     install-sh  Makefile       share
build.sh      config.h.in    configure.in  iv_def.h    Makefile.in    src
chkstream.m4  config.log     Copyright     libtool     mkinstalldirs  x86_64
conf13883.sh  config.status  include       ltmain.sh   name

[phendric@hpc-login2 iv]$ ls include
Dispatch    IV-2_6   ivstream.h  ivversion.h  OS
InterViews  IV-look  ivstrm.h    IV-X11       TIFF

[phendric@hpc-login2 iv]$ ls x86_64/lib/
libIVhines.la    libIVhines.so.3.0.3  libUnidrawhines.so.3
libIVhines.so    libUnidrawhines.la   libUnidrawhines.so.3.0.3
libIVhines.so.3  libUnidrawhines.so

[phendric@hpc-login2 iv]$ 
Those same files are located on my local laptop, on which I had no such problem compiling NEURON. I know I'm probably just overlooking something simple, but does anyone have an idea about why NEURON can't find the IV files when they clearly exist? I'm following the compilation instructions on the NEURON website, so under $HOME/nrn70, I have the directories iv & nrn. NEURON should know exactly where to look, but for some reason, it's not seeing what's there.

Thanks,
Phillip

PS - for now, because I want to get up and running quickly, I'm compiling NEURON without interviews, but I want to know what's causing the error.

hines
Site Admin
Posts: 1599
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON can't find IV headers/libs

Post by hines »

You said where you installed iv but now where you tried to install neuron.
And you did not give the configure args you used for neuron.
You probably installed iv in a non-default looked for location relative to neuron.

hines
Site Admin
Posts: 1599
Joined: Wed May 18, 2005 3:32 pm

Re: NEURON can't find IV headers/libs

Post by hines »

Actually, one would need to know the configure args for iv as well. Relative means relative to the <prefix> of the installations.

phendric
Posts: 18
Joined: Tue Apr 21, 2009 12:57 am

Re: NEURON can't find IV headers/libs

Post by phendric »

Michael,

Under /home/rcf-proj3/tb/phendric/nrn70/ I have two directories: iv & nrn.

From within /home/rcf-proj3/tb/phendric/nrn70/iv I run

Code: Select all

./configure --prefix=`pwd`
make
make install
As far as I can tell from the output, the compilation process for Interviews completes successfully. I then navigate to /home/rcf-proj3/tb/phendric/nrn70/nrn and run the following:

Code: Select all

./configure --prefix=`pwd` --with-mpi --with-iv=/home/rcf-proj3/tb/phendric/nrn70/iv
Halfway through the configure process, I get the "can't find interviews" error that I mentioned in the original post. This happens regardless of whether I include the '--with-iv=' option or not.

Phillip

phendric
Posts: 18
Joined: Tue Apr 21, 2009 12:57 am

Re: NEURON can't find IV headers/libs

Post by phendric »

Another update:

I tried compiling NEURON without any graphical interface...

Code: Select all

./configure --prefix=`pwd` --with-mpi --without-x
When I came back an hour later, I found that the build process had failed with several errors. I'm including the last part of the output, but you can see that there are multiple places where loops get vectorized (should that happen?), warnings pop up about headers that are deprecated, and while the output here doesn't show it, I saw several places where warnings popped up about implicit function calls being made. All of these warnings look foreign to me - should they be coming up?
make[3]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/ivoc'
Making all in nrncvode
make[3]: Entering directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/nrncvode'
make all-am
make[4]: Entering directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/nrncvode'
make[4]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/nrncvode'
make[3]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/nrncvode'
Making all in parallel
make[3]: Entering directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/parallel'
make all-am
make[4]: Entering directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/parallel'
make[4]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/parallel'
make[3]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/parallel'
Making all in nrniv
make[3]: Entering directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/nrniv'
if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT nrnmenu.lo -MD -MP -MF ".deps/nrnmenu.Tpo" -c -o nrnmenu.lo nrnmenu.cpp; \
then mv -f ".deps/nrnmenu.Tpo" ".deps/nrnmenu.Plo"; else rm -f ".deps/nrnmenu.Tpo"; exit 1; fi
mkdir .libs
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT nrnmenu.lo -MD -MP -MF .deps/nrnmenu.Tpo -c nrnmenu.cpp -fPIC -DPIC -o .libs/nrnmenu.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT shape.lo -MD -MP -MF ".deps/shape.Tpo" -c -o shape.lo shape.cpp; \
then mv -f ".deps/shape.Tpo" ".deps/shape.Plo"; else rm -f ".deps/shape.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT shape.lo -MD -MP -MF .deps/shape.Tpo -c shape.cpp -fPIC -DPIC -o .libs/shape.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT classreg.lo -MD -MP -MF ".deps/classreg.Tpo" -c -o classreg.lo classreg.cpp; \
then mv -f ".deps/classreg.Tpo" ".deps/classreg.Plo"; else rm -f ".deps/classreg.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT classreg.lo -MD -MP -MF .deps/classreg.Tpo -c classreg.cpp -fPIC -DPIC -o .libs/classreg.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT rotate3d.lo -MD -MP -MF ".deps/rotate3d.Tpo" -c -o rotate3d.lo rotate3d.cpp; \
then mv -f ".deps/rotate3d.Tpo" ".deps/rotate3d.Plo"; else rm -f ".deps/rotate3d.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT rotate3d.lo -MD -MP -MF .deps/rotate3d.Tpo -c rotate3d.cpp -fPIC -DPIC -o .libs/rotate3d.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT datapath.lo -MD -MP -MF ".deps/datapath.Tpo" -c -o datapath.lo datapath.cpp; \
then mv -f ".deps/datapath.Tpo" ".deps/datapath.Plo"; else rm -f ".deps/datapath.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT datapath.lo -MD -MP -MF .deps/datapath.Tpo -c datapath.cpp -fPIC -DPIC -o .libs/datapath.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT symdir.lo -MD -MP -MF ".deps/symdir.Tpo" -c -o symdir.lo symdir.cpp; \
then mv -f ".deps/symdir.Tpo" ".deps/symdir.Plo"; else rm -f ".deps/symdir.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT symdir.lo -MD -MP -MF .deps/symdir.Tpo -c symdir.cpp -fPIC -DPIC -o .libs/symdir.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

../ivoc/symdir.cpp(327): warning #269: invalid format string conversion
sprintf(tmp, "%.*%s%.*%s", s1.length(), s1.string(), s2.length(), s2.string());
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT spaceplt.lo -MD -MP -MF ".deps/spaceplt.Tpo" -c -o spaceplt.lo spaceplt.cpp; \
then mv -f ".deps/spaceplt.Tpo" ".deps/spaceplt.Plo"; else rm -f ".deps/spaceplt.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT spaceplt.lo -MD -MP -MF .deps/spaceplt.Tpo -c spaceplt.cpp -fPIC -DPIC -o .libs/spaceplt.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT shapeplt.lo -MD -MP -MF ".deps/shapeplt.Tpo" -c -o shapeplt.lo shapeplt.cpp; \
then mv -f ".deps/shapeplt.Tpo" ".deps/shapeplt.Plo"; else rm -f ".deps/shapeplt.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT shapeplt.lo -MD -MP -MF .deps/shapeplt.Tpo -c shapeplt.cpp -fPIC -DPIC -o .libs/shapeplt.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT ppshape.lo -MD -MP -MF ".deps/ppshape.Tpo" -c -o ppshape.lo ppshape.cpp; \
then mv -f ".deps/ppshape.Tpo" ".deps/ppshape.Plo"; else rm -f ".deps/ppshape.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT ppshape.lo -MD -MP -MF .deps/ppshape.Tpo -c ppshape.cpp -fPIC -DPIC -o .libs/ppshape.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT secbrows.lo -MD -MP -MF ".deps/secbrows.Tpo" -c -o secbrows.lo secbrows.cpp; \
then mv -f ".deps/secbrows.Tpo" ".deps/secbrows.Plo"; else rm -f ".deps/secbrows.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT secbrows.lo -MD -MP -MF .deps/secbrows.Tpo -c secbrows.cpp -fPIC -DPIC -o .libs/secbrows.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT ndatclas.lo -MD -MP -MF ".deps/ndatclas.Tpo" -c -o ndatclas.lo ndatclas.cpp; \
then mv -f ".deps/ndatclas.Tpo" ".deps/ndatclas.Plo"; else rm -f ".deps/ndatclas.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT ndatclas.lo -MD -MP -MF .deps/ndatclas.Tpo -c ndatclas.cpp -fPIC -DPIC -o .libs/ndatclas.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

ndatclas.cpp(178): (col. 6) remark: LOOP WAS VECTORIZED.
if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT impedanc.lo -MD -MP -MF ".deps/impedanc.Tpo" -c -o impedanc.lo impedanc.cpp; \
then mv -f ".deps/impedanc.Tpo" ".deps/impedanc.Plo"; else rm -f ".deps/impedanc.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT impedanc.lo -MD -MP -MF .deps/impedanc.Tpo -c impedanc.cpp -fPIC -DPIC -o .libs/impedanc.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT savstate.lo -MD -MP -MF ".deps/savstate.Tpo" -c -o savstate.lo savstate.cpp; \
then mv -f ".deps/savstate.Tpo" ".deps/savstate.Plo"; else rm -f ".deps/savstate.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT savstate.lo -MD -MP -MF .deps/savstate.Tpo -c savstate.cpp -fPIC -DPIC -o .libs/savstate.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

savstate.cpp(842): (col. 3) remark: LOOP WAS VECTORIZED.
if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT hocmech.lo -MD -MP -MF ".deps/hocmech.Tpo" -c -o hocmech.lo hocmech.cpp; \
then mv -f ".deps/hocmech.Tpo" ".deps/hocmech.Plo"; else rm -f ".deps/hocmech.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT hocmech.lo -MD -MP -MF .deps/hocmech.Tpo -c hocmech.cpp -fPIC -DPIC -o .libs/hocmech.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT ocjump.lo -MD -MP -MF ".deps/ocjump.Tpo" -c -o ocjump.lo ocjump.cpp; \
then mv -f ".deps/ocjump.Tpo" ".deps/ocjump.Plo"; else rm -f ".deps/ocjump.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT ocjump.lo -MD -MP -MF .deps/ocjump.Tpo -c ocjump.cpp -fPIC -DPIC -o .libs/ocjump.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT vrecord.lo -MD -MP -MF ".deps/vrecord.Tpo" -c -o vrecord.lo vrecord.cpp; \
then mv -f ".deps/vrecord.Tpo" ".deps/vrecord.Plo"; else rm -f ".deps/vrecord.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT vrecord.lo -MD -MP -MF .deps/vrecord.Tpo -c vrecord.cpp -fPIC -DPIC -o .libs/vrecord.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT cvodestb.lo -MD -MP -MF ".deps/cvodestb.Tpo" -c -o cvodestb.lo cvodestb.cpp; \
then mv -f ".deps/cvodestb.Tpo" ".deps/cvodestb.Plo"; else rm -f ".deps/cvodestb.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT cvodestb.lo -MD -MP -MF .deps/cvodestb.Tpo -c cvodestb.cpp -fPIC -DPIC -o .libs/cvodestb.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT occvode.lo -MD -MP -MF ".deps/occvode.Tpo" -c -o occvode.lo occvode.cpp; \
then mv -f ".deps/occvode.Tpo" ".deps/occvode.Plo"; else rm -f ".deps/occvode.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT occvode.lo -MD -MP -MF .deps/occvode.Tpo -c occvode.cpp -fPIC -DPIC -o .libs/occvode.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT cvodeobj.lo -MD -MP -MF ".deps/cvodeobj.Tpo" -c -o cvodeobj.lo cvodeobj.cpp; \
then mv -f ".deps/cvodeobj.Tpo" ".deps/cvodeobj.Plo"; else rm -f ".deps/cvodeobj.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT cvodeobj.lo -MD -MP -MF .deps/cvodeobj.Tpo -c cvodeobj.cpp -fPIC -DPIC -o .libs/cvodeobj.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

../nrncvode/cvodeobj.cpp(869): (col. 3) remark: LOOP WAS VECTORIZED.
../nrncvode/cvodeobj.cpp(854): (col. 3) remark: LOOP WAS VECTORIZED.
if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT cvtrset.lo -MD -MP -MF ".deps/cvtrset.Tpo" -c -o cvtrset.lo cvtrset.cpp; \
then mv -f ".deps/cvtrset.Tpo" ".deps/cvtrset.Plo"; else rm -f ".deps/cvtrset.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT cvtrset.lo -MD -MP -MF .deps/cvtrset.Tpo -c cvtrset.cpp -fPIC -DPIC -o .libs/cvtrset.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT tqueue.lo -MD -MP -MF ".deps/tqueue.Tpo" -c -o tqueue.lo tqueue.cpp; \
then mv -f ".deps/tqueue.Tpo" ".deps/tqueue.Plo"; else rm -f ".deps/tqueue.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT tqueue.lo -MD -MP -MF .deps/tqueue.Tpo -c tqueue.cpp -fPIC -DPIC -o .libs/tqueue.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

if /bin/sh ../../libtool --tag=CXX --mode=compile mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT netcvode.lo -MD -MP -MF ".deps/netcvode.Tpo" -c -o netcvode.lo netcvode.cpp; \
then mv -f ".deps/netcvode.Tpo" ".deps/netcvode.Plo"; else rm -f ".deps/netcvode.Tpo"; exit 1; fi
mpicxx -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../.. -I../../src/oc -I../../src/oc -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I../../src/nrnpython -I../../src/sundials -I../../src/sundials/shared -I../../src/nrncvode -I../../src/sparse13 -I../../src/gnu -I. -I../../src/ivoc -I../../src/nrnoc -I../../src/oc -I../../src/oc -I../../src/ivos -I../../src/parallel -I../../src/nrnmpi -DOOP=1 -DCABLE=1 -DUSECVODE=1 -DUSEMATRIX=1 -DUSEBBS=1 -g -O2 -MT netcvode.lo -MD -MP -MF .deps/netcvode.Tpo -c netcvode.cpp -fPIC -DPIC -o .libs/netcvode.o
/usr/include/c++/4.1.2/backward/backward_warning.h(32): warning #1224: #warning directive: This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
#warning This file includes at least one deprecated or antiquated header. \
^

../../src/gnu/d_vec.h(64): error: "map" has already been declared in the current scope
friend doubleVec& map(doubleMapper f, doubleVec & a);
^

../nrncvode/netcvode.cpp(4768): warning #181: argument is incompatible with corresponding format string conversion
fprintf(f, "%d\n", presyn_->hi_index_);
^

compilation aborted for netcvode.cpp (code 2)
make[3]: *** [netcvode.lo] Error 1
make[3]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src/nrniv'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/auto/rcf-proj3/tb/phendric/nrn70/nrn'
make: *** [all] Error 2
A little about the tools & the compiler:

Code: Select all

[phendric@hpc-login2 ~]$ gcc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-44)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
They're running gcc version 4.1.2.

Code: Select all

[phendric@hpc-login2 ~]$ mpicc --version
icc (ICC) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[phendric@hpc-login2 ~]$ which mpicc
/usr/usc/mpich/1.2.7..7/mx-intel/bin/mpicc
They're using MPICH v1.2.7 (so it's not MPICH2)...and it's an Intel-produced version (mx-intel).

And, finally, the OS version:

Code: Select all

[phendric@hpc-login2 ~]$ cat /etc/issue
CentOS release 5.3 (Final)
Kernel \r on an \m
Any suggestions about what the problem is & how to fix it?

Thanks,
Phillip

Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

Re: NEURON can't find IV headers/libs

Post by Keivan »

I do not have experience of using mpich or centOS but I have some using mpich2, icc and ubuntu.
from errors and waring it is appear that your mpicc trying to compile neuron with icc --> you told that. to be sure did you installed icc and set the correct environment variables? as I remember hines told me he had difficulty installing intel compilers on his centOS.
as a comment --> try the latest development code --> may help.
you should compile iv and nrn with icc and icpc
------
ps: it may sound hackneyed --> but I think you could not use iv in the cluster environment.
ps: excuse me if I'm interfering.

phendric
Posts: 18
Joined: Tue Apr 21, 2009 12:57 am

Re: NEURON can't find IV headers/libs

Post by phendric »

Keivan,

Genius - the problem was, in fact, due to the Intel compiler. The cluster I'm on has another compiler available to use...so I'm using it:

Code: Select all

[phendric@hpc-login2 CA1Model]$ gcc --version
gcc (GCC) 4.3.3
Copyright (C) 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
and

Code: Select all

[phendric@hpc-login2 CA1Model]$ mpicc --version
gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-44)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
NEURON now compiles quickly and beautifully WITHOUT Interviews. However, when I try to configure it to compile with IV, I'm still getting the error that NEURON can't find IV.
...
checking compilation with interviews... failed
I can't compile and/or link an interviews program. If InterViews is not
installed in /usr or /usr/local or /usr/local/iv,
specify the proper location of the interviews tree using

configure --with-iv=/where/you/put/iv

The interviews headers should be in subdirectories of
/where/you/put/iv/include, and the libraries should be in
/where/you/put/iv/lib or /where/you/put/iv/x86_64/lib
(not in /where/you/put/iv/lib/ALPHA or
/where/you/put/iv/lib/LINUX or some other subdirectory of lib).

If you don't want interviews, but do want nrniv built with the non-gui
c++ classes then specify configure --without-iv.
I wish I knew why this is happening...It's not critical that I fix it, as I can run NEURON without Interviews on the cluster, but it'd be nice to know what's going on, nonetheless.

Phillip

Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

Re: NEURON can't find IV headers/libs

Post by Keivan »

mpicc is not really a compiler its just an script act like compilers. In fact, I think it uses the compiler originally used to compile it. --> try this

use the command

Code: Select all

make uninstall && make distclean 
to clean both iv and nrn directories then compile again as I told you before.
If you want to keep your existing mpich you should install intel compilers then compile iv and nrn with it.
if you cannot install intel compilers, you should compile mpich, iv and nrn with gcc.
I recommend icc because of it superior speed. I recommend following compiler flags also.

Code: Select all

-O2 -ipo
do not use -fast and -O3

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