About compiling cp2k

Phil Song ys... at bu.edu
Tue Apr 17 14:29:47 UTC 2012
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Roger:

Thank you so much for your help! I was able to compile cp2k without
the fftw3 wrapper (setup attached later).
It seemed that using the "-mkl" flag to include the libraries is more
robust than using "-lmkl_XXX".

Again, thank you so much!

Best,
Phil

==================================================================
MKL = /usr/local/intel/composer_xe_2011_sp1.9.293/mkl
MKL_INC = $(MKL)/include/fftw
MKL_LIB = $(MKL)/lib/intel64

CC       = icc
CPP      =
FC       = ifort
LD       = ifort
AR       = xiar -r
DFLAGS   = -D__INTEL -D__FFTSG -D__FFTW3 -D__FFTMKL
CPPFLAGS = -C -traditional $(DFLAGS) -I$(MKL_INC)
FCFLAGS  = $(DFLAGS) -I$(MKL_INC) -O2 -xHost -heap-arrays 64 -fpp -
free
FCFLAGS2 = $(DFLAGS) -I$(MKL_INC) -O1 -xHost -heap-arrays 64 -fpp -
free
LDFLAGS  = $(FCFLAGS)

LIBS     = -L$(MKL_LIB) -mkl

OBJECTS_ARCHITECTURE = machine_intel.o

graphcon.o: graphcon.F
        $(FC) -c $(FCFLAGS2) $<

qs_vxc_atom.o: qs_vxc_atom.F
        $(FC) -c $(FCFLAGS2) $<
==================================================================

On Apr 17, 5:48 am, nadler <rod... at gmx.ch> wrote:
> Hi Phil,
>
> Try to reduce the optimization flags, this helped me to get rid of the
> segmentation faults with earlier versions of ifort. Start with -O0 and if
> the error disappears, try -O2 which should be enough. Then also, if you use
> the arch file as you've posted it you should move the part
>
> MKL = /usr/local/intel/composer_xe_2011_sp1.9.293/mkl
> MKL_INC = $(MKL)/include/fftw
> MKL_LIB = $(MKL)/lib/intel64
>
> INTEL_MKL_LIB=$(HOME)/cp2k/fftw3xf
>
> to the top of the file. Otherwise  -I$(MKL_INC) has nothing to include.
> With the new Intel compilers the FFTW is now contained in the MKL library
> directly and there is no need to build the wrapper:http://software.intel.com/en-us/articles/build-cp2k-using-intel-fortr...
>
> I hope this helps.
>
> Regards,
> Roger
>
>
>
>
>
>
>
> On Monday, April 16, 2012 9:27:47 PM UTC+2, Phil Song wrote:
>
> > Hi, all:
>
> > I am trying to compile cp2k serial version with the newest intel
> > fortran compiler (64 Compiler XE Version 12.1.3.293 Build 20120212).
> > And I have used a config file (attached later) for compiling, where I
> > have compiled the fftw3 that comes with the intel MKL library and put
> > it on $(HOME)/cp2k/fftw3xf for linking (because I am not the
> > administrator of the cluster). Both the compiling and linking went
> > smoothly.
>
> > However, when I tried to run one of the test example in the cp2k/tests/
> > QS directory. The program crashed in the middle of the run after
> > display "QUICKSTEP" with a segmentation fault (SIGSEGV). I have tried
> > to open up a debugger to see what happened and I have found that the
> > segmentation fault was originated from the following stack:
>
> > ===========================================================================
>
> > #0  0x00007f575fcfb985 in mkl_blas_dgemm_mscale () in /usr/local/intel/
> > composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_mc3.so
> > #1  0x00007f576245b9a5 in mkl_blas_dgemm_mscale () in /usr/local/intel/
> > composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_core.so
> > #2  0x00007f575ffa5313 in mkl_blas_xdgemm () in /usr/local/intel/
> > composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_mc3.so
> > #3  0x00007f576245d369 in mkl_blas_xdgemm () in /usr/local/intel/
> > composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_core.so
> > #4  0x00007f5763485dff in mkl_blas_dgemm () in /usr/local/intel/
> > composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_sequential.so
> > #5  0x00007f5763bbf11b in dgemm () in /usr/local/intel/
> > composer_xe_2011_sp1.9.293/mkl/lib/intel64/libmkl_intel_ilp64.so
> > #6  0x0000000000ecdb8a in basis_set_types_mp_init_orb_basis_set_ ()
> > in /home/ysong/cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #7  0x0000000000eaf716 in atomic_kind_types_mp_init_atomic_kind_set_
> > () in /home/ysong/cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #8  0x0000000001629043 in qs_environment_mp_qs_init_subsys_ () in /
> > home/ysong/cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #9  0x000000000163023f in qs_environment_mp_qs_init_ () in /home/ysong/
> > cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #10 0x000000000085b35c in qs_main_mp_quickstep_create_force_env_ ()
> > in /home/ysong/cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #11 0x0000000000465341 in f77_interface_mp_create_force_env_ () in /
> > home/ysong/cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #12 0x000000000040bc8a in cp2k_runs_mp_cp2k_run_ () in /home/ysong/
> > cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #13 0x000000000040ae44 in cp2k_runs_mp_run_input_ () in /home/ysong/
> > cp2k/cp2k-2.2/exe/Linux-x86-64-intel/cp2k.sopt
> > #14 0x0000000000407a06 in MAIN__ () in /home/ysong/cp2k/cp2k-2.2/exe/
> > Linux-x86-64-intel/cp2k.sopt
> > ===========================================================================
>
> > I was trying to further debug the cp2k source code to figure out where
> > the problems came from. But it seemed that the parameters passed to
> > basis_set_types_mp_init_orb_basis_set seemed all right. Therefore, I
> > am very confused. Could this be a problem with the newest MKL, which I
> > think is unlikely? Or could this be a bug in the cp2k source? Or could
> > I did not compile and link the program correctly?
>
> > I have spent quite a long time look at this and still could not solve
> > it. I hope someone can help me with this and any suggestion will be
> > greatly appreciated.
>
> > Thanks a lot!
>
> > Best,
> > Phil Song
>
> > The machine that I have used to compile cp2k is equipped with a quad
> > core i7 920.
>
> > The config file Linux-x86-64-intel.sopt for compilation is attached as
> > follow.
>
> > ===========================================================================
>
> > CC       = icc
> > CPP      =
> > FC       = ifort
> > LD       = ifort
> > AR       = xiar -r
> > DFLAGS   = -D__INTEL -D__FFTSG -D__FFTW3 -D__FFTMKL
> > CPPFLAGS = -C -traditional $(DFLAGS) -I$(MKL_INC)
> > FCFLAGS  = $(DFLAGS) -I$(MKL_INC) -O3 -xHost -heap-arrays 64 -fpp -
> > free
> > FCFLAGS2 = $(DFLAGS) -I$(MKL_INC) -O1 -xHost -heap-arrays 64 -fpp -
> > free
> > LDFLAGS  = $(FCFLAGS)
>
> > MKL = /usr/local/intel/composer_xe_2011_sp1.9.293/mkl
> > MKL_INC = $(MKL)/include/fftw
> > MKL_LIB = $(MKL)/lib/intel64
>
> > INTEL_MKL_LIB=$(HOME)/cp2k/fftw3xf
>
> > LIBS     = -L$(MKL_LIB) -L$(INTEL_MKL_LIB) \
> >            -lfftw3xf_intel \
> >            -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm
>
> > OBJECTS_ARCHITECTURE = machine_intel.o
>
> > graphcon.o: graphcon.F
> >         $(FC) -c $(FCFLAGS2) $<
>
> > qs_vxc_atom.o: qs_vxc_atom.F
> >         $(FC) -c $(FCFLAGS2) $<
> > ===========================================================================
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