Hi Maduka,
I have not seen this specific error before BUT I have seen similar things
occur when the whole of AMBER is not built with the same compiler. E.g. you
start with the Intel compilers for the CPU code and then switch to GNU for
the cuda code. This can cause strange errors because netcdf.mod is not
rebuilt with the new compiler. Make clean also does not clean this out.
I would suggest starting from a completely clean untar of AMBER 12. Then try
to build just the cuda code and see if that works. So essentially:
tar xvjf Amber12.tar.bz2
tar xvjf AmberTools12.tar.bz2
export AMBERHOME=/current path/amber12
cd $AMBERHOME
./configure -cuda gnu
./configure -cuda gnu (Yes you have to run configure twice to make sure it
applies all the patches.)
make install
See if that works.
All the best
Ross
From: Maduka Ogba [mailto:maduka.ogba.gmail.com]
Sent: Wednesday, June 20, 2012 4:57 PM
To: amber-owner.ambermd.org
Subject: Problem with installing Amber 12 CUDA GPU version (NetCDF error)
Dear Amber Owner,
I am having problems installing the GPU version of amber 12. I have
installed and used both the serial and parallel CPU version of Amber
extensively but I am still getting this error message after the make command
for cuda. I have installed CUDA and have the correct NVIDIA driver required
for GPU support. My configuration file ***seems*** fine but I get the error
at the end of the file that states "Fatal Error: Wrong module version '6'
(expected '0') for file 'netcdf.mod' opened at (1)".
I appreciate a solution to this issue as I would love to take advantage of
the GPU capabilities of Amber as soon as possible.
**Command line code and results copied and paste below**
**user command is in bold font**
Best Regards,
Maduka
----------------------------------------------------------------------------
----------------------------------------------------------------------------
---------------------
./configure -cuda gnu
Checking for updates...
AmberTools12 is up to date
Amber12 is up to date
Searching for python2... Found python2.7: /usr/bin/python2.7
Obtaining the gnu suite version:
gcc -v
The version is 4.4.7
Testing the gcc compiler:
gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c
OK
Testing the gfortran compiler:
gfortran -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
gfortran -O0 -c -o testp.f.o testp.f
gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Configuring NetCDF (may be time-consuming)...
NetCDF configure succeeded.
Checking for zlib: OK
Checking for libbz2: OK
Skipping configuration of FFTW3
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
dukes.Transformer-2 ~/amber12 % make install
cd AmberTools/src && make install
make[1]: Entering directory `/home/dukes/amber12/AmberTools/src'
AmberTools12 has no CUDA-enabled components
(cd ../../src && make cuda )
make[2]: Entering directory `/home/dukes/amber12/src'
Starting installation of Amber12 (cuda) at Wed Jun 20 16:33:31 PDT 2012.
cd pmemd && make cuda
make[3]: Entering directory `/home/dukes/amber12/src/pmemd'
make -C src/ cuda
make[4]: Entering directory `/home/dukes/amber12/src/pmemd/src'
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c gbl_constants.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c gbl_datatypes.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c state_info.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c file_io_dat.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c pmemd_lib.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c parallel_dat.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c file_io.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c mdin_ctrl_dat.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c axis_optimize.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c fft1d.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c charmm.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c nextprmtop_section.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c prmtop_dat.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c mdin_ewald_dat.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c mdin_debugf_dat.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c remd.F90
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c binrestart.F90
binrestart.F90:48.13:
use netcdf
1
Fatal Error: Wrong module version '6' (expected '0') for file 'netcdf.mod'
opened at (1)
make[4]: *** [binrestart.o] Error 1
make[4]: Leaving directory `/home/dukes/amber12/src/pmemd/src'
make[3]: *** [cuda] Error 2
make[3]: Leaving directory `/home/dukes/amber12/src/pmemd'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/dukes/amber12/src'
make[1]: [cuda] Error 2 (ignored)
make[1]: Leaving directory `/home/dukes/amber12/AmberTools/src'
make[1]: Entering directory `/home/dukes/amber12/src'
Starting installation of Amber12 (cuda) at Wed Jun 20 16:33:34 PDT 2012.
cd pmemd && make cuda
make[2]: Entering directory `/home/dukes/amber12/src/pmemd'
make -C src/ cuda
make[3]: Entering directory `/home/dukes/amber12/src/pmemd/src'
gfortran -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
-DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA
-I/home/dukes/amber12/include -c binrestart.F90
binrestart.F90:48.13:
use netcdf
1
Fatal Error: Wrong module version '6' (expected '0') for file 'netcdf.mod'
opened at (1)
make[3]: *** [binrestart.o] Error 1
make[3]: Leaving directory `/home/dukes/amber12/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/home/dukes/amber12/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/home/dukes/amber12/src'
make: *** [install] Error 2
----------------------------------------------------------------------------
-------------------------------------------------------
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Received on Wed Jun 20 2012 - 17:30:02 PDT
