Below is the output. It can be fixed by adding
"-I/opt/apps/intel/13/composer_xe_2013.2.146/mkl/include/fftw" to the right
locations, I think. --Niel
$ ./configure -noX11 -noemil -nomtkpp -norism -nofftw3 intel
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
No patches available
Available Amber 15 patches:
No patches available
Searching for python2... Found python2.7:
/opt/apps/python/epd/7.3.2/bin/python2.7
Detected icc version 13
Detected ifort version 13
Using Intel MKL libraries in
/opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64
MKL Version 10 or greater assumed.
Testing the icc compiler:
icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the icpc compiler:
icpc -fpic -o testp testp.cpp
OK
Testing the ifort compiler:
ifort -fpic -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
ifort -fpic -O0 -c -o testp.f.o testp.f
icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c.o testp.f.o -lifport -lifcore -lsvml
OK
Testing pointer size:
icc -fpic -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Checking NetCDF...
Using bundled NetCDF library.
Using existing NetCDF in '/work/01168/henrikse/amber-intel'
Checking for zlib: OK
Checking for libbz2: OK
Configuring MKL FFTW for PMEMD...
MKL_HOME set to /opt/apps/intel/13/composer_xe_2013.2.146/mkl
Skipping configuration of FFTW3
The configuration file, config.h, was successfully created.
--------------------------------------------------------------------------------
Environment resource files are provided to set the proper environment
variables to use AMBER and AmberTools.
If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
/home1/01168/henrikse/work/amber-intel/amber.sh file in your shell.
Consider adding the line
test -f /home1/01168/henrikse/work/amber-intel/amber.sh && source
/home1/01168/henrikse/work/amber-intel/amber.sh
to your startup file (e.g., ~/.bashrc)
If you use a C shell (e.g., csh, tcsh), source the
/home1/01168/henrikse/work/amber-intel/amber.csh file in your shell.
Consider adding the line
test -f /home1/01168/henrikse/work/amber-intel/amber.csh && source
/home1/01168/henrikse/work/amber-intel/amber.csh
to your startup file (e.g., ~/.cshrc)
--------------------------------------------------------------------------------
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
[henrikse.login1 amber-intel]$ cd src/
[henrikse.login1 src]$ make install
Starting installation of Amber14 (serial) at Mon Oct 13 14:15:35 CDT 2014.
cd pmemd && make install
make[1]: Entering directory `/work/01168/henrikse/amber-intel/src/pmemd'
make -C src/ install
make[2]: Entering directory `/work/01168/henrikse/amber-intel/src/pmemd/src'
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c gbl_constants.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c gbl_datatypes.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c state_info.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c file_io_dat.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c axis_optimize.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c -o AmberNetcdf.o
../../../AmberTools/src/lib/AmberNetcdf.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c
nextprmtop_section.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c energy_records.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c constantph_dat.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c bspline.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c veclib.F90
icc -ipo -O3 -no-prec-div -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DBINTRAJ -DFFTW_FFT -I/work/01168/henrikse/amber-intel/include -c
pmemd_clib.c
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c erfcfun.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c pmemd_lib.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c parallel_dat.F90
ifort -DMKL -DBINTRAJ -DFFTW_FFT -DMKL_FFTW_FFT -ipo -O3 -no-prec-div
-xHost -I/work/01168/henrikse/amber-intel/include -c fft1d.F90
fft1d.F90(33): #error: can't find include file: fftw3.f
make[2]: *** [fft1d.o] Error 1
On Mon, Oct 13, 2014 at 1:05 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Mon, Oct 13, 2014, Niel Henriksen wrote:
> >
> > I noticed that in the current GIT version of Amber, compiling fails if
> you
> > use MKL libraries and the "-nofftw3" option together. Perhaps MKL is
> only
> > used for fftw and thus specifying these two options is silly, but in case
> > that's not true, I thought I'd share.
>
> For Niel: what is the error?
>
> For everyone, but especially Tyler: do we need the -nofftw3 option
> anymore?
> How about flags like -norism, -nosse, -g95, -phenix, ....
>
> ....dac
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
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Received on Mon Oct 13 2014 - 14:00:02 PDT
