Problems to compile NEURON on Mac Xgrid
Posted: Wed May 20, 2009 9:43 am
Hi,
We are trying to run NEURON 7.0 on a local network of seven eight-core Macs running MacOSX (10.4 &.5). The grid is controlled by apple's Xgrid software which creates a directory on a local mac for each job (with user name nobody), assigning random names.
Unfortunately, it isn't possible to have the jobs use the ordinary NEURON installations of the macs (/Applications/NEURON...), for lack of access (that's a precondition coming from how the xgrid works, according to the person who manages the system).
Thus, what I've tried to do is to install neuron in the new, randomly named, local directory for each job. To have it recognize the path of this directory, compilation of the source code is necessary since the standard installation refers to "/Applications/NEURON.."
It works fine to compile and install NEURON in any directory on the macs when the compilation and installation is done locally. The script I use is this, from http://www.neuron.yale.edu/neuron/insta ... d_osx.html:
#!/bin/bash
export localXgridSessionDir=$(pwd)
export localNRNdir=$localXgridSessionDir/NEURON-7.0
export PATH=$PATH:$localXgridSessionDir:$localNRNdir/nrn/umac/bin
IDIR=$localNRNdir
mkdir neuron
mv iv-17.tar.gz neuron
mv nrn-7.0.tar.gz neuron
cd neuron
tar xzf iv-17.tar.gz
cd iv-17
./configure --prefix=$IDIR/iv --enable-carbon
make
make install
cd $localXgridSessionDir/neuron
tar xzf nrn-7.0.tar.gz
cd nrn-7.0
./configure --prefix=$IDIR/nrn --with-iv=$IDIR/iv --enable-carbon
make
make install
make after_install
However, when we repeat the procedure on the xgrid, the compiler gets stuck and returns this error message:
configure: error: sources are in ., but `cd .' does not work
make: *** No targets specified and no makefile found. Stop.
configure: error: sources are in ., but `cd .' does not work
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target `after_install'. Stop.
The manager of the system says that this is due to the NEURON configuration using a restricted shell with limited rights (which for example can not cd, as shown in the above error message).
Any ideas about solving this would be very much appreciated!
Thanks,
Joe
We are trying to run NEURON 7.0 on a local network of seven eight-core Macs running MacOSX (10.4 &.5). The grid is controlled by apple's Xgrid software which creates a directory on a local mac for each job (with user name nobody), assigning random names.
Unfortunately, it isn't possible to have the jobs use the ordinary NEURON installations of the macs (/Applications/NEURON...), for lack of access (that's a precondition coming from how the xgrid works, according to the person who manages the system).
Thus, what I've tried to do is to install neuron in the new, randomly named, local directory for each job. To have it recognize the path of this directory, compilation of the source code is necessary since the standard installation refers to "/Applications/NEURON.."
It works fine to compile and install NEURON in any directory on the macs when the compilation and installation is done locally. The script I use is this, from http://www.neuron.yale.edu/neuron/insta ... d_osx.html:
#!/bin/bash
export localXgridSessionDir=$(pwd)
export localNRNdir=$localXgridSessionDir/NEURON-7.0
export PATH=$PATH:$localXgridSessionDir:$localNRNdir/nrn/umac/bin
IDIR=$localNRNdir
mkdir neuron
mv iv-17.tar.gz neuron
mv nrn-7.0.tar.gz neuron
cd neuron
tar xzf iv-17.tar.gz
cd iv-17
./configure --prefix=$IDIR/iv --enable-carbon
make
make install
cd $localXgridSessionDir/neuron
tar xzf nrn-7.0.tar.gz
cd nrn-7.0
./configure --prefix=$IDIR/nrn --with-iv=$IDIR/iv --enable-carbon
make
make install
make after_install
However, when we repeat the procedure on the xgrid, the compiler gets stuck and returns this error message:
configure: error: sources are in ., but `cd .' does not work
make: *** No targets specified and no makefile found. Stop.
configure: error: sources are in ., but `cd .' does not work
make: *** No targets specified and no makefile found. Stop.
make: *** No rule to make target `after_install'. Stop.
The manager of the system says that this is due to the NEURON configuration using a restricted shell with limited rights (which for example can not cd, as shown in the above error message).
Any ideas about solving this would be very much appreciated!
Thanks,
Joe