Re: [AMBER-Developers] -j x parallel builds broken if you don't build serial first

From: Jason Swails <>
Date: Wed, 27 Mar 2013 14:15:57 -0400

On Wed, Mar 27, 2013 at 2:03 PM, Ross Walker <> wrote:

> Something looks to be messed up with the netcdf dependencies.
> The following works:
> git pull
> git clean -f -d -x
> ./configure gnu
> make -j8 install
> make clean
> ./configure -cuda gnu
> make -j8 install
> But the following does not:
> git clean -f -d -x
> ./configure -cuda gnu
> make -j8 install
> gfortran -I../libsrc -I. -O3 -mtune=native -c -o typeSizes.o typeSizes.f90
> gfortran -I../libsrc -I. -O3 -mtune=native -c -o netcdf.o netcdf.f90
> netcdf.f90:38.50:
> FourByteReal, EightByteReal
> 1
> Fatal Error: Can't open module file 'typesizes.mod' for reading at (1): No
> such file or directory
> make[4]: *** [netcdf.o] Error 1
> make[4]: *** Waiting for unfinished jobs....
> gfortran -I../libsrc -I. -O3 -mtune=native -c netcdf.f90 -o netcdf.o
> gfortran -I../libsrc -I. -O3 -mtune=native -c typeSizes.f90 -o typeSizes.o
> make[4]: Leaving directory
> `/server-home1/rcw/cvs_checkouts/amber.git/amber/AmberTools/src/netcdf/src/
> f90'
> make[3]: *** [install-recursive] Error 1
> make[3]: Leaving directory
> `/server-home1/rcw/cvs_checkouts/amber.git/amber/AmberTools/src/netcdf/src'
> make[2]: *** [/home/rcw/cvs_checkouts/amber.git/amber/include/netcdf.mod]
> Error 2
> make[2]: Leaving directory
> `/server-home1/rcw/cvs_checkouts/amber.git/amber/src'
> make[1]: [cuda] Error 2 (ignored)
> Any ideas?

This is a race condition in the NetCDF install, I think. I don't see this
every time (and the fewer threads you use, the less frequently this
occurs). It also happens more often on large, parallel file systems where
file access time is less reliable.

I checked in a fix that basically hard-codes the NetCDF build (only) to a
single thread. If someone wants to go through the NetCDF build and fix the
dependencies themselves to remove this restriction, they're more than
welcome ;).

Try it now? If it fixes the issue then I'll cherry-pick that commit over
to the amber13-with-patches branch.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Wed Mar 27 2013 - 11:30:05 PDT
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