[CP2K:3789] Re: About compiling cp2k

Alin M Elena alinm... at gmail.com
Tue Apr 17 14:54:50 UTC 2012
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Dear Phil,

-mkl is just a shorthand for some libs that intel decided for you to bundle 
and make life easier...  (thread, programming model and computational kernel) 
Using that one needs to check what is brought in... and see if intel made the 
right choice.
using -lmkl_xxxx you have to know what you want... and the freedom to achieve 
it. The one that I see strange in your arch file is this ilp64 for the 
programming model. why did you chose it?

can you post a ldd on your generated binary please?

the "robust" way to get what you want is -mkl=sequential
a simple test on one of my machines shows me that -mkl 
links to a threaded version of mkl and not sequential
[alin at abbaton:~/playground/2dIntegration/source]: ldd a 
        linux-vdso.so.1 (0x00007fffe39ff000)
        libmkl_intel_lp64.so => 
/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/libmkl_intel_lp64.so 
(0x00007fcd00fdb000)
        libmkl_intel_thread.so => 
/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/libmkl_intel_thread.so 
(0x00007fccfff89000)
        libmkl_core.so => 
/opt/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64/libmkl_core.so 
(0x00007fccfef4f000)
        libiomp5.so => 
/opt/intel/composer_xe_2011_sp1.7.256/compiler/lib/intel64/libiomp5.so 
(0x00007fccfec63000)
        libm.so.6 => /lib64/libm.so.6 (0x00007fccfe96d000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fccfe751000)
        libc.so.6 => /lib64/libc.so.6 (0x00007fccfe3ad000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fccfe197000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007fccfdf93000)
        /lib64/ld-linux-x86-64.so.2 (0x00007fcd0177c000)

regards,
Alin




On Tue 17 Apr 2012 07:29:47 Phil Song wrote:
> 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-f
> > ortr...
> > 
> > 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) $<
> > > 
========================================================================
> > > ===
-- 
Without Questions there are no Answers!
______________________________________________________________________
Alin Marin ELENA
Advanced Molecular Simulation Research Laboratory
School of Physics, University College Dublin
----
Ardionsamblú Móilíneach Saotharlann Taighde
Scoil na Fisice, An Coláiste Ollscoile, Baile Átha Cliath

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http://alin.elenaworld.net
______________________________________________________________________
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