[AMBER] NETCDF Installation Error

From: Ali Faruqi <alifar76.gmail.com>
Date: Wed, 29 Jun 2011 16:10:02 +0500

Dear Users,

I have been able to successfuly install AmberTools, version 1.3. I got the
following message after installation.

Installation of AmberTools, version 1.3 is complete at Mon Jun 27 14:48:00
PKT 2011.

However, when I attempt to configure amber10 with g95, as instructed in the
installation manual, I encounter this message:

Setting AMBERHOME to /home/AMBER-backup/Amber10/amber10
Setting up Amber configuration file for architecture: g95
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
Testing the C compiler:
      gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64 -o testp
Testing the Fortran compiler:
     g95 -O0 -fno-second-underscore -o testp testp.f
  ------ Configuring the netCDF libraries: --------
Configuring netcdf; (may be time-consuming)
./configure_amber: line 1211: cd: netcdf/src: No such file or directory
netcdf configure returned 1
NETCDF configure failed! Check the netcdf_config.log file

The src directory of Amber10 does not contain any netcdf sub-directory upon
unpacking from tar file. The netcdf_config.log file present in the src
sub-directory of the AmberTools directory shows nothing unusual, as
AmberTools was installed successfully.
One way round this problem was to use the '-nobintraj' flag which does not
include support for binary (netCDF) trajectory files. This allowed
successful installation of Amber10. However, I do not know what impact will
exclusion of binary trajectory files have on the results of the simulation I
will perform later on. I also tried to pool the contents of the src
directory of both AmberTools and Amber10 in one directory and tried to
generate the config.h, with the following command:

./configure_amber -static g95

I did not face the 'No such file or directory' Error but ended up getting
'No F90 Compiler' Error, which I have also mentioned in one of my previous

Configuring netcdf; (may be time-consuming)
configure: WARNING: No F90 compiler found. F90 API will not be built.
configure: error: Could not link conftestf.o and conftest.o
netcdf configure returned 1
NETCDF configure failed! Check the netcdf_config.log file

It is surprising as I have g95 properly installed on my system. I used the
gfortran compiler instead of g95 to make the config.h file with the command:

./configure_amber -static gfortran

I faced no error. But when I issue the 'make serial' command, I get the
sander compilation error which I have explained in my previous post:

su-sander-proxy.o ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o
                ../lapack/lapack.a ../blas/blas.a \
                ../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
gfortran: ../lapack/lapack.a: No such file or directory
gfortran: ../blas/blas.a: No such file or directory
make[1]: *** [sander] Error 1
make[1]: Leaving directory `/home/AMBER-backup/Amber-10/amber10/src/sander'
make: *** [serial] Error 2

I would really appreciate someone can guide me in this regard as I am a
complete beginner at AMBER and have no guide/instructor. Thank you very

Ali A. Faruqi
Karachi, Pakistan
AMBER mailing list
Received on Wed Jun 29 2011 - 04:30:03 PDT
Custom Search