First of all, thanks everybody for the help. ;)
Yang, I know, I know. I should keep to the GNU. But lets say that I get addicted to the intel compiler on a cpmd winter school, when it appeared in front of me as the only freely available for both amd and intel cpus fortran90 compiler. Since it also came with performance for free, that was a good deal. I also have just a handfull of tuning flags I use for icc and ifort. But, like everybody in here, we choose the machines for performance (which means, first corret result, and later speed), same goes for me for the compilers. Moreover, as I said before: I wana try QM/MM, and CPMD doesn't work with gcc.
Back to the subject: David, thanks for the piece of gmx4 code. Unfortunatelly, it don't work. I deleted all the objects from the directory before trying to compile to assure that, and it yelded the same error.
On the other hand, the trick of compiling just mknb in gcc, and the rest with icc got a bit farther, before crashing... but still gone with about a thousand of weird warnings. I'm sending the window desktop outputs attached in this message. Anyway, in order to make that trick, I've used the following "script":
****************************************************************************************************
export CPPFLAGS=-I/usr/local/lib64/fftw/gnu/include
export LDFLAGS=-L/usr/local/lib64/fftw/gnu/lib
export CC=/usr/local/bin/gcc
export CFLAGS="-O3 -ffast-math -funroll-all-loops -fpeel-loops"
make distclean
./configure --prefix=/usr/local/bin/chemistry/gromacs/ISI/ --with-fft=fftw3
cp ./src/gmxlib/nonbonded/nb_kernel/Makefile ./Makefile.mknb.gcc
cp ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile ./Makefile.mknb_kernel_ia32_3dnow.gcc
cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile ./Makefile.mknb_kernel_ia32_sse.gcc
cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile ./Makefile.mknb_kernel_ia32_sse2.gcc
cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile ./Makefile.mknb_kernel_x86_64_sse.gcc
cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile ./Makefile.mknb_kernel_x86_64_sse2.gcc
export PATH="$PATH /usr/local/intel/bin/ . /usr/local/intel/lib/"
export LD_LIBRARY_PATH=/usr/local/intel/lib/
export CPPFLAGS=-I/usr/local/lib64/fftw/intel/include
export LDFLAGS=-L/usr/local/lib64/fftw/intel/lib
export CC=/usr/local/intel/bin/icc
export CXX=/usr/local/intel/bin/icpc
export F77=/usr/local/intel/bin/ifort
export CFLAGS=" "
export CXXFLAGS=" "
export FFLAGS=" "
export CFLAGS="-O3 -axP -xW -ipo -static "
export CXXFLAGS="-O3 -axP -xW -ipo -static "
export FFLAGS="-O3 -axP -xW -ipo -static "
make distclean
./configure --prefix=/usr/local/bin/chemistry/gromacs/ISI/ --with-fft=fftw3 --disable-x86-64-sse
cp ./src/gmxlib/nonbonded/nb_kernel/Makefile ./Makefile.mknb.icc
cp ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile ./Makefile.mknb_kernel_ia32_3dnow.icc
cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile ./Makefile.mknb_kernel_ia32_sse.icc
cp ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile ./Makefile.mknb_kernel_ia32_sse2.icc
cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile ./Makefile.mknb_kernel_x86_64_sse.icc
cp ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile ./Makefile.mknb_kernel_x86_64_sse2.icc
cp ./Makefile.mknb.gcc ./src/gmxlib/nonbonded/nb_kernel/Makefile
cp ./Makefile.mknb_kernel_ia32_3dnow.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile
cp ./Makefile.mknb_kernel_ia32_sse.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile
cp ./Makefile.mknb_kernel_ia32_sse2.gcc ./src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile
cp ./Makefile.mknb_kernel_x86_64_sse.gcc ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile
cp ./Makefile.mknb_kernel_x86_64_sse2.gcc ./src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile
make
****************************************************************************************************
The output from it isn't attached. :( Sorry, The gziped file is too big for the list limits. Anyway, despite lots of warnings, the compilations ends dieing in here:
*********************************************************************************************
/tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function'
/tmp/ipo_iccpmJSXr.o(.text+0x2edde):/tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function'
/tmp/ipo_iccpmJSXr.o(.text+0x2ede6):/tmp/ipo_iccpmJSXr.c: undefined reference to `interaction_function'
/tmp/ipo_iccpmJSXr.o(.text+0x2f1ca):/tmp/ipo_iccpmJSXr.c: undefined reference to `_gmx_error'
/tmp/ipo_iccpmJSXr.o(.text+0x2f29b): In function `DS_Init':
/tmp/ipo_iccpmJSXr.c: undefined reference to `save_calloc'
/tmp/ipo_iccpmJSXr.o(.text+0x2f64d):/tmp/ipo_iccpmJSXr.c: undefined reference to `debug'
/tmp/ipo_iccpmJSXr.o(.text+0x2f682):/tmp/ipo_iccpmJSXr.c: undefined reference to `debug'
/tmp/ipo_iccpmJSXr.o(.text+0x2f6f6):/tmp/ipo_iccpmJSXr.c: undefined reference to `debug'
/tmp/ipo_iccpmJSXr.o(.text+0x2f76c): In function `init_block2':
/tmp/ipo_iccpmJSXr.c: undefined reference to `save_calloc'
/tmp/ipo_iccpmJSXr.o(.text+0x2f78d):/tmp/ipo_iccpmJSXr.c: undefined reference to `save_calloc'
make[3]: ** [grompp] Erro 1
make[3]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'
make[1]: ** [all] Erro 2
make[1]: Leaving directory `/home/johannes/src/gromacs/gromacs-3.3/src'
make: ** [all-recursive] Erro 1
**********************************************************************************************
Trying withou the "-ipo" flag now. It still yelds the same weird warning (warning #147: declaration is incompatible with "double invsqrt(double)" (declared at line 565 of "/usr/local/intel/include/math.h")
static inline real invsqrt(real x)) and shows a lot of warnings like these before stopping:
**********************************************************************************************
ld: skipping incompatible /usr/X11/lib/libXmu.so when searching for -lXmu
ld: skipping incompatible /usr/X11/lib/libXmu.a when searching for -lXmu
ld: skipping incompatible /usr/X11R6/lib/libXmu.so when searching for -lXmu
ld: skipping incompatible /usr/X11R6/lib/libXmu.a when searching for -lXmu
ld: skipping incompatible /usr/X11/lib/libSM.so when searching for -lSM
ld: skipping incompatible /usr/X11/lib/libSM.a when searching for -lSM
ld: skipping incompatible /usr/X11R6/lib/libSM.so when searching for -lSM
ld: skipping incompatible /usr/X11R6/lib/libSM.a when searching for -lSM
ld: skipping incompatible /usr/X11/lib/libICE.so when searching for -lICE
ld: skipping incompatible /usr/X11/lib/libICE.a when searching for -lICE
ld: skipping incompatible /usr/X11R6/lib/libICE.so when searching for -lICE
ld: skipping incompatible /usr/X11R6/lib/libICE.a when searching for -lICE
ld: skipping incompatible /usr/X11/lib/libXext.so when searching for -lXext
ld: skipping incompatible /usr/X11/lib/libXext.a when searching for -lXext
ld: skipping incompatible /usr/X11R6/lib/libXext.so when searching for -lXext
ld: skipping incompatible /usr/X11R6/lib/libXext.a when searching for -lXext
ld: skipping incompatible /usr/X11/lib/libXp.so when searching for -lXp
ld: skipping incompatible /usr/X11/lib/libXp.a when searching for -lXp
ld: skipping incompatible /usr/X11R6/lib/libXp.so when searching for -lXp
ld: skipping incompatible /usr/X11R6/lib/libXp.a when searching for -lXp
ld: skipping incompatible /usr/X11/lib/libXt.so when searching for -lXt
ld: skipping incompatible /usr/X11/lib/libXt.a when searching for -lXt
ld: skipping incompatible /usr/X11R6/lib/libXt.so when searching for -lXt
ld: skipping incompatible /usr/X11R6/lib/libXt.a when searching for -lXt
ld: skipping incompatible /usr/X11/lib/libX11.so when searching for -lX11
ld: skipping incompatible /usr/X11/lib/libX11.a when searching for -lX11
ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11
ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11
**********************************************************************************************
I don't know why, but I got the feeling that this is the most promissing stuff up to now! :) But what are those warnings and errors?
Tom, just did as suggest with gdb. The output follows:
*****************************************************************
GNU gdb 6.3
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "x86_64-suse-linux"...Using host libthread_db library "/lib64/tls/libthread_db.so.1".
(gdb) r -software_invsqrt
Starting program: /home/johannes/src/gromacs/gromacs-3.3/src/gmxlib/nonbonded/nb_kernel/mknb -software_invsqrt
>>> Gromacs nonbonded kernel generator (-h for help)
>>> Generating single precision functions in C.
>>> Using Gromacs software version of 1/sqrt(x).
Program received signal SIGSEGV, Segmentation fault.
0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6
(gdb) bt
#0 0x00002aaaab15a88c in __find_specmb () from /lib64/tls/libc.so.6
#1 0x00002aaaab140e6f in vfprintf () from /lib64/tls/libc.so.6
#2 0x00002aaaab15e2a9 in vsprintf () from /lib64/tls/libc.so.6
#3 0x00002aaaab149568 in sprintf () from /lib64/tls/libc.so.6
#4 0x0000000000402a47 in mknb_code ()
#5 0x0000000000402183 in mknb_declare_int ()
#6 0x000000000040356d in mknb_declare_variables ()
#7 0x0000000000401989 in main ()
**********************************************************************
Seems to yeld the same as before... :( Any bell ringing?
People, really sorry for bothering the whole list with this subject. I would not do so if I didn't want to give a try for the gromacs+cpmd combo. Also, I do think that if this can be done, more people will be able to get results from this (even if the results is "don't try, it doesn't yeld you any performance improve on AMD machines", it will at least let others without any doubt if the trial would be usefull)
Thanks in advance for everything.
Jones
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