[CP2K:2500] Re: Test files -H2O
Teodoro Laino
teodor... at gmail.com
Fri Jan 8 06:21:16 UTC 2010
It is very difficult to help when the help is not clear.
Looks like again this is an intel related problem: or you provide
extensive information or you will hardly get any help.
Most important: look at the old posts on Intel or even better change
compiler.
Teo
Amit Patel wrote:
> I have the same issue. any help ??
>
> -Amit
>
> On Jan 7, 4:52 pm, Sandeep Kumar Reddy <kuma... at gmail.com> wrote:
>
>> Hello,
>> i tried with this arch and it compiled successfully. But when i ran
>> the test jobs, it got stopped during the SCF cycle.( It hasn't done a single
>> SCF step but it is runnning without any output) .
>> The arch. file that i used to compile the serial version is
>>
>> Make file "Linux-x86-64-intel-jnc.sopt"
>>
>> CC = cc
>> CPP =
>> FC = ifort
>> LD = ifort
>>
>> AR = ar -r
>> DFLAGS = -D__INTEL -D__FFTSG -D_FFTW3
>> # -D__FFTACML
>> # -D_FFTSG
>> INTEL_INC = -I/sfs1/intel_122009/Compiler/11.1/059/mkl/include
>> -I/sfs3/home/amit/compilledpackages/fftw-3.2.2/installed/include
>> INTEL_LIB = /sfs1/intel_122009/Compiler/11.1/059/mkl/lib/em64t
>> MKLPATH = /sfs1/intel_122009/Compiler/11.1/059/mkl/lib/em64t
>> FFTW3_LIB = /sfs3/home/amit/compilledpackages/fftw-3.2.2/installed/lib
>>
>> CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
>> FCFLAGS = $(DFLAGS) -I$(INTEL_INC) -O2 -xW -heap-arrays 64 -fpp -free
>> FCFLAGS2 = $(DFLAGS) -I$(INTEL_INC) -O1 -xW -heap-arrays 64 -fpp -free
>>
>> LDFLAGS = $(FCFLAGS)
>> LIBS = $(MKLPATH)/libmkl_solver_lp64.a -Wl,--start-group
>> $(MKLPATH)/libmkl_intel_lp64.a $(MKLPATH)/libmkl_sequential.a
>> $(MKLPATH)/libmkl_core.a -Wl,--end-group -lpthread -lguide
>> $(FFTW3_LIB)/libfftw3.a
>>
>> Any help?
>>
>> Thank you,
>>
>> Regards,
>> Sandeep kumar reddy
>>
>> On Thu, Jan 7, 2010 at 5:36 AM, J�rg Sa�mannshausen <
>>
>> jorg.sassm... at strath.ac.uk> wrote:
>>
>>> Dear Sandeep
>>>
>>> how does your arch file look like?
>>>
>>> Reading this:
>>>
>>> http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/cp2k/INSTALL?view=mark...
>>>
>>> I am wondering whether you might have forgotten to swap the -D__FFTW3 with
>>> the -D__FFTACML (as you are using the ACML FFT) flag.
>>>
>>> Just a guess of course ;-)
>>>
>>> All the best
>>>
>>> J�rg
>>>
>>> On Mittwoch 06 Januar 2010 Sandeep Kumar Reddy wrote:
>>>
>>>> Hello sir,
>>>> When i try to compile with popt, I got these error.
>>>>
>>>> mkl_sequential.a
>>>> /sfs1/intel_122009/Compiler/11.1/059/mkl/lib/em64t/libmkl_core.a
>>>> -Wl,--end-group -lpthread -lguide
>>>>
>>> /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
>>> (.text+0xadf): In function `fftacml3d_':
>>>
>>>> : undefined reference to `zfft3dx_'
>>>>
>>> /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
>>> (.text+0xb47): In function `fftacml3d_':
>>>
>>>> : undefined reference to `zfft3dx_'
>>>>
>>> /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
>>> (.text+0xdb0): In function `fftacml1dm_':
>>>
>>>> : undefined reference to `zfft1mx_'
>>>>
>>> /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
>>> (.text+0xe2b): In function `fftacml1dm_':
>>>
>>>> : undefined reference to `zfft1mx_'
>>>>
>>>> I don't know what this error means. Could you help me ?
>>>>
>>>> Regards,
>>>> Sandeep kumar reddy
>>>>
>>>> On Wed, Jan 6, 2010 at 1:56 PM, Teodoro Laino
>>>> <teodor... at gmail.com<mailto:teodor... at gmail.com>> wrote: Hello,
>>>>
>>>> If I would be you I would first try to check if a popt works! If it is
>>>> working (with same compiler/libraries setup) then I would go for trying
>>>>
>>> the
>>>
>>>> psmp.
>>>>
>>>> Teo
>>>>
>>>> Sandeep Kumar Reddy wrote:
>>>> Hello,
>>>>
>>>> Thank you for your quick reply. Following are the details about
>>>> compilers, arch etc.
>>>>
>>>> Intel Compiler(ifort) Version : 10.1
>>>>
>>>> My Arch File : "Linux-x86-64-intel.psmp"
>>>>
>>>> # by default some intel compilers put temporaries on the stack
>>>> # this might lead to segmentation faults is the stack limit is set to low
>>>> # stack limits can be increased by sysadmins or e.g with ulimit -s 256000
>>>> # furthermore new ifort (10.0?) compilers support the option
>>>> # -heap-arrays 64
>>>> # add this to the compilation flags is the other options do not work
>>>> # The following settings worked for:
>>>> # - AMD64 Opteron
>>>> # - SUSE Linux Enterprise Server 10.0 (x86_64)
>>>> # - Intel(R) Fortran Compiler for Intel(R) EM64T-based applications,
>>>> Version 10.0 # - AMD acml library version 3.6.0
>>>> # - MPICH2-1.0.5p4
>>>> # - FFTW 3.1.2
>>>> #
>>>> CC = cc
>>>> CPP =
>>>> FC = ifort -openmp -FR -O0
>>>> LD = ifort -openmp -FR -O0
>>>> AR = ar -r
>>>> DFLAGS = -D__INTEL -D__FFTSG -D__FFTW3
>>>> CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
>>>> INTEL_INC= -I/sfs1/intel_012008/mkl/10.0.011/include
>>>> -I/sfs1/intel_012008/mkl/10.0.011/include/fftw INTEL_LIB=
>>>> /sfs1/intel_012008/mkl/10.0.011/lib/em64t
>>>> FCFLAGS = $(DFLAGS) $(INTEL_INC) -heap-arrays 64
>>>> FCFLAGS2 = $(DFLAGS) $(INTEL_INC) -heap-arrays 64
>>>> LDFLAGS = $(FCFLAGS) -i-static
>>>> MKLPATH = /sfs1/intel_012008/mkl/10.0.011/lib/em64t/
>>>> LIBS = -L$(MKLPATH) -lfftw3xf_intel $(MKLPATH)/libmkl_solver_lp64.a
>>>> -Wl,--start-group $(MKLPATH)/libmkl_intel_lp64.a
>>>> $(MKLPATH)/libmkl_intel_thread.a $(M KLPATH)/libmkl_core.a
>>>>
>>> -Wl,--end-group
>>>
>>>> -openmp -lpthread
>>>>
>>>> # $(INTEL_LIB)/libmkl_scalapack_lp64.a \
>>>>
>>>> # $(INTEL_LIB)/libmkl_core.a \
>>>>
>>>> # $(INTEL_LIB)/libfftw3.a
>>>>
>>>> OBJECTS_ARCHITECTURE = machine_intel.o
>>>>
>>>> graphcon.o: graphcon.F
>>>> $(FC) -c $(FCFLAGS2) $<
>>>> Linux-jnc.psmp (END)
>>>>
>>>> Regards,
>>>> Sandeep kumar reddy
>>>>
>>>> On Wed, Jan 6, 2010 at 12:27 PM, Laino Teodoro
>>>> <teodor... at gmail.com<mailto:teodor... at gmail.com>
>>>> <mailto:teodor... at gmail.com<mailto:teodor... at gmail.com>>> wrote:
>>>>
>>>> Hello Sandeep,
>>>>
>>>> your executable is giving almost random numbers:
>>>>
>>>> 1 P_Mix/Diag. 0.40E+00 0.3 1.96524988
>>>>
>>> -17.0390500821
>>>
>>>> -1.70E+01 2 P_Mix/Diag. 0.40E+00 0.4 1.17914993
>>>> -13.5426292836 3.50E+00 3 P_Mix/Diag. 0.40E+00 0.4 0.70748996
>>>> -9.9067192962 3.64E+00 4 P_Mix/Diag. 0.40E+00 0.4 0.42449397
>>>> -7.1955092465 2.71E+00 5 P_Mix/Diag. 0.40E+00 0.4
>>>>
>>> 0.25469638
>>>
>>>> -5.3903907002 1.81E+00
>>>>
>>>> while a correct executable should give more reasonable numbers:
>>>>
>>>> 1 P_Mix/Diag. 0.40E+00 0.7 0.94986401
>>>>
>>> -17.0390500821
>>>
>>>> -1.70E+01 2 P_Mix/Diag. 0.40E+00 0.7 0.55704339
>>>> -17.1017974052 -6.27E-02 3 P_Mix/Diag. 0.40E+00 0.8 0.33374888
>>>> -17.1395184934 -3.77E-02 4 P_Mix/Diag. 0.40E+00 0.8 0.19743634
>>>> -17.1616212665 -2.21E-02 5 P_Mix/Diag. 0.40E+00 0.9
>>>>
>>> 0.11691752
>>>
>>>> -17.1746976329 -1.31E-02
>>>>
>>>> (Please check the 6th column)
>>>>
>>>> You need to provide your arch file, compiler, version, libraries
>>>> and first of all look through all the past messages to see if
>>>> somebody experienced the same problem you have (very probably you
>>>> have a bugged compiler version or wrong libraries).
>>>>
>>>> Teo
>>>>
>>>> On 6 Jan 2010, at 07:47, Sandeep Kumar Reddy wrote:
>>>>
>>>> Hello,
>>>> Please help a new user of CP2K. I am trying to learn
>>>> CP2K. When i try to execute H2O.inp given in tests directory
>>>> of cp2k, the output file terminated after reading the contents
>>>> of the input file. I am using a serial executable. Following
>>>> is the input file.
>>>>
>>>> &FORCE_EVAL
>>>> METHOD Quickstep
>>>> &DFT
>>>> &MGRID
>>>> CUTOFF 280
>>>> &END MGRID
>>>> &QS
>>>> EPS_DEFAULT 1.0E-12
>>>> &END QS
>>>> &SCF
>>>> SCF_GUESS ATOMIC
>>>> EPS_SCF 3.0E-7
>>>> MAX_SCF 50
>>>> &DIAGONALIZATION
>>>> ALGORITHM STANDARD
>>>> &END DIAGONALIZATION
>>>> &END SCF
>>>> &XC
>>>> &XC_FUNCTIONAL BLYP
>>>> &END XC_FUNCTIONAL
>>>> &END XC
>>>> &END DFT
>>>> &SUBSYS
>>>> &CELL
>>>> ABC 5.0 5.0 5.0
>>>> &END CELL
>>>> &COORD
>>>> O 0.000000 0.000000 -0.065587
>>>> H 0.000000 -0.757136 0.520545
>>>> H 0.000000 0.757136 0.520545
>>>> &END COORD
>>>> &KIND H
>>>> BASIS_SET DZVP-GTH-BLYP
>>>> POTENTIAL GTH-BLYP-q1
>>>> &END KIND
>>>> &KIND O
>>>> BASIS_SET DZVP-GTH-BLYP
>>>> POTENTIAL GTH-BLYP-q6
>>>> &END KIND
>>>> &END SUBSYS
>>>> &END FORCE_EVAL
>>>> &GLOBAL
>>>> PROJECT H2O
>>>> RUN_TYPE ENERGY_FORCE
>>>> PRINT_LEVEL MEDIUM
>>>> &END GLOBAL
>>>>
>>>> The output file is
>>>> ----------------------------
>>>>
>>>> SCF PARAMETERS Density guess:
>>>> ATOMIC
>>>>
>>> --------------------------------------------------------
>>>
>>>> max_scf: 50
>>>> max_scf_history: 0 max_diis:
>>>> 4
>>>> -------------------------------------------------------- eps_scf:
>>>> 3.00E-07 eps_scf_history:
>>>> 0.00E+00 eps_diis:
>>>> 1.00E-01 eps_eigval:
>>>> 1.00E-05 --------------------------------------------------------
>>>> level_shift [a.u.]: 0.00
>>>> -------------------------------------------------------- Mixing method:
>>>> DIRECT_P_MIXING
>>>> -------------------------------------------------------- No outer SCF
>>>>
>>>> PW_GRID: Information for grid number
>>>> 1 PW_GRID: Cutoff [a.u.]
>>>> 140.0 PW_GRID: spherical cutoff:
>>>> NO PW_GRID: Bounds 1
>>>> -27 26 Points: 54 PW_GRID: Bounds
>>>>
>>> 2
>>>
>>>> -27 26 Points: 54 PW_GRID:
>>>> Bounds 3
>>>>
>> ...
>>
>> read more �
>>
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