Introduction :
CP2K (http://cp2k.berlios.de/) is a freely available (GPL) program, written in Fortran, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
Version :
1.08
Obtaining Source Code :
CP2K stable version
- the cp2k-2_1-branch: ftp://ftp.berlios.de/pub/cp2k/cp2k-2_1-branch.tar.gz
- the cp2k-2_2-branch: ftp://ftp.berlios.de/pub/cp2k/cp2k-2_2-branch.tar.gz
CP2K development version
- (nightly snapshot): ftp://ftp.berlios.de/pub/cp2k/cp2k.tar.gz
Prerequisites :
CP2K requires that you already have installed the Fortran compiler, math library with FFTW 2.x/3.x support. We suggest using both Intel Fortran compiler and Intel Math Kernel Library for better performance.
Configuration Set Up :
n/a
Source Code Changes :
n/a
Building the Application :
Here we show the detail on how to build the CP2K source with Intel Fortran Compiler for Intel 64 platform.
Part I. Intel Fortran Composer XE 2011
1) Download and install Intel Fortran Composer XE 2011 (first release version 2011.0.084).
Make sure you select to install both Intel Fortran compiler and Intel Math Kernel Library (MKL). The default installation directory is /opt/intel/composerxe-2011/ .
2) Build FFTW version 3.x wrappers library for Intel MKL Library
From Intel MKL version 10.2 and later, FFTW3 interface for Intel Fortran compiler is pre-built and ntegrated in Intel MKL core libraries. See /en-us/articles/intel-mkl-main-libraries-contain-fftw3-interfaces.
Source code is still available to create wrappers for use with other compilers. Here is example to build Fortran version by gnu compiler.
3) Untar the CP2K.tar.gz, and modify configuration file “Linux-x86-64-intel.sopt” in cp2k/arch directory, which is targeting for Intel 64 platform.
Here is an example of Linux-x86-64-intel.sopt for reference:
4) Setup the environment of Intel Fortran compiler, then build CP2K source:
Part II. Intel Fortran Compiler Professional Edition (version 11.0 / 11.1)
Please follow the steps listing below:.
1) Download and install Intel Fortran compiler Professional Edition version.
Make sure you select to install both Intel Fortran compiler and Intel Math Kernel Library (MKL). For example, the default installation directory is under /opt/intel/Compiler/11.0/083 or /opt/intel/Compiler/11.1/072.
2) Build FFTW version 3.x wrappers library for Intel MKL Library
Note: Please skip this step if you are using Intel Fortran compiler version 11.1, or Intel MKL libraries version 10.2 and later.
The source code for the wrappers and makefiles with the wrapper list files for Fortran are located in the /interfaces/fftw3xf sub-directories in the Intel MKL directory. Please use Intel C++ compiler (or GCC) to generate the wrappers library (libffw3xf_intel.a, or libfftw3xf_gnu.a):
3) Untar the CP2K.tar.gz, and modify configuration file “Linux-x86-64-intel.sopt” in cp2k/arch directory, which is targeting for Intel 64 platform.
Here is an example of Linux-x86-64-intel.sopt for reference:
4) Setup the environment of Intel Fortran compiler, then build CP2K source:
Running the Application :
CP2K provide several test cases, which can be used for stability testing and verify the results to see if the compilation is correct.
Known Issues or Limitations :
1) For CP2K version 2.1 branch
We recommended to use Intel Fortran Compiler version 11.1 update 6 (version 11.1.072) or later version.
If you want to use new Intel Fortran Composer XE 2011 (aka version 12.0), we suggest that one source file "qs_vxc_atom.F" should be compiled with -O1 option only. You could add the following lines into Linux-x86-64-intel.sopt to avoid this problem:
2) For CP2K version 2.2 branch
Suggested to use the Intel Fortran compiler 11.1 update 6 and later version.
There are some known issues with new Composer XE 2011 (ifort version 12.x.xxx). Please use the XE 2011 update 8 and future version, also apply the following patches in configuration file "Linux-x86-64-intel.sopt":
<end>
- DPD200161616
- DPD200172602
Version :
1.08
Obtaining Source Code :
CP2K stable version
- the cp2k-2_1-branch: ftp://ftp.berlios.de/pub/cp2k/cp2k-2_1-branch.tar.gz
- the cp2k-2_2-branch: ftp://ftp.berlios.de/pub/cp2k/cp2k-2_2-branch.tar.gz
CP2K development version
- (nightly snapshot): ftp://ftp.berlios.de/pub/cp2k/cp2k.tar.gz
Prerequisites :
CP2K requires that you already have installed the Fortran compiler, math library with FFTW 2.x/3.x support. We suggest using both Intel Fortran compiler and Intel Math Kernel Library for better performance.
Configuration Set Up :
n/a
Source Code Changes :
n/a
Building the Application :
Here we show the detail on how to build the CP2K source with Intel Fortran Compiler for Intel 64 platform.
Part I. Intel Fortran Composer XE 2011
1) Download and install Intel Fortran Composer XE 2011 (first release version 2011.0.084).
Make sure you select to install both Intel Fortran compiler and Intel Math Kernel Library (MKL). The default installation directory is /opt/intel/composerxe-2011/ .
2) Build FFTW version 3.x wrappers library for Intel MKL Library
From Intel MKL version 10.2 and later, FFTW3 interface for Intel Fortran compiler is pre-built and ntegrated in Intel MKL core libraries. See /en-us/articles/intel-mkl-main-libraries-contain-fftw3-interfaces.
Source code is still available to create wrappers for use with other compilers. Here is example to build Fortran version by gnu compiler.
] cd /opt/intel/composerxe-2011/mkl/interfaces/fftw3xf
] make libintel64 compiler=gnu
3) Untar the CP2K.tar.gz, and modify configuration file “Linux-x86-64-intel.sopt” in cp2k/arch directory, which is targeting for Intel 64 platform.
Here is an example of Linux-x86-64-intel.sopt for reference:
INTEL_MKL = /opt/intel/composerxe-2011/mklNotice: The options (-O2 -xHost) are available for both Intel® and non-Intel microprocessors but it may result in more optimizations for Intel microprocessors than for non-Intel microprocessors.
INTEL_INC = $(INTEL_MKL)/include/fftw
INTEL_LIB = $(INTEL_MKL)/lib/intel64
LIBINT_PATH = /usr/lib/libint-1.1.4
LIBINT_LIB = $(LIBINT_PATH)/lib/libderiv.a $(LIBINT_PATH)/lib/libint.a -lstdc++
FC = ifort
LD = ifort
AR = xiar -r
DFLAGS = -D__INTEL -D__FFTSG -D__FFTW3 -D__FFTMKL -D__LIBINT
CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
FCFLAGS = $(DFLAGS) -I$(INTEL_INC) -O2 -xHost -heap-arrays 64 -fpp -free
LDFLAGS = $(FCFLAGS)
#LIBS = -mkl
LIBS = -L$(INTEL_LIB) -mkl $(LIBINT_LIB)
OBJECTS_ARCHITECTURE = machine_intel.o
4) Setup the environment of Intel Fortran compiler, then build CP2K source:
] source /opt/intel/composerxe-2011/bin/compilervars.sh intel64
] cd cp2k/makefiles/
] make ARCH=Linux-x86-64-intel VERSION=sopt
Part II. Intel Fortran Compiler Professional Edition (version 11.0 / 11.1)
Please follow the steps listing below:.
1) Download and install Intel Fortran compiler Professional Edition version.
Make sure you select to install both Intel Fortran compiler and Intel Math Kernel Library (MKL). For example, the default installation directory is under /opt/intel/Compiler/11.0/083 or /opt/intel/Compiler/11.1/072.
2) Build FFTW version 3.x wrappers library for Intel MKL Library
Note: Please skip this step if you are using Intel Fortran compiler version 11.1, or Intel MKL libraries version 10.2 and later.
The source code for the wrappers and makefiles with the wrapper list files for Fortran are located in the /interfaces/fftw3xf sub-directories in the Intel MKL directory. Please use Intel C++ compiler (or GCC) to generate the wrappers library (libffw3xf_intel.a, or libfftw3xf_gnu.a):
] cd /opt/intel/Compiler/11.0/083/mkl/interfaces/fftw3xf
] make libem64t compiler=intel (or make libem64t compiler=gnu)
3) Untar the CP2K.tar.gz, and modify configuration file “Linux-x86-64-intel.sopt” in cp2k/arch directory, which is targeting for Intel 64 platform.
Here is an example of Linux-x86-64-intel.sopt for reference:
INTEL_MKL = /opt/intel/Compiler/11.0/083/mklNotice: The options (-O2 -xHost) are available for both Intel® and non-Intel microprocessors but it may result in more optimizations for Intel microprocessors than for non-Intel microprocessors.
INTEL_INC = $(INTEL_MKL)/include/fftw
INTEL_LIB = $(INTEL_MKL)/lib/em64t
FC = ifort
LD = ifort
AR = xiar -r
DFLAGS = -D__INTEL -D__FFTSG -D__FFTW3 -D__FFTMKL
CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
FCFLAGS = $(DFLAGS) -I$(INTEL_INC) -O2 -xHost -heap-arrays 64 -fpp -free
LDFLAGS = $(FCFLAGS)
# If you are using ifort verison 11.1 with MKL version 10.2 and later, Intel MKL libraries and FFTW interfaces will be linked automatically with -mkl option
# LIBS = -L$(INTEL_LIB) -mkl
LIBS = -L$(INTEL_LIB) -lfftw3xf_intel -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
OBJECTS_ARCHITECTURE = machine_intel.o
4) Setup the environment of Intel Fortran compiler, then build CP2K source:
] source /opt/intel/Compiler/11.0/083/bin/ifortvars.sh intel64
] cd cp2k/makefiles/
] make ARCH=Linux-x86-64-intel VERSION=sopt
Running the Application :
CP2K provide several test cases, which can be used for stability testing and verify the results to see if the compilation is correct.
] cd cp2k/tests/QS
] ./../../exe/Linux-x86-64-intel/cp2k.sopt H2O-32.inp
] ./../../exe/Linux-x86-64-intel/cp2k.sopt H2O-3x3.inp
Known Issues or Limitations :
1) For CP2K version 2.1 branch
We recommended to use Intel Fortran Compiler version 11.1 update 6 (version 11.1.072) or later version.
If you want to use new Intel Fortran Composer XE 2011 (aka version 12.0), we suggest that one source file "qs_vxc_atom.F" should be compiled with -O1 option only. You could add the following lines into Linux-x86-64-intel.sopt to avoid this problem:
FCFLAGS2 = -I$(INTEL_INC) -O1 -xHost -heap-arrays 64 -fpp -free $(DFLAGS)
qs_vxc_atom.o: qs_vxc_atom.F
$(FC) -c $(FCFLAGS2) $<
2) For CP2K version 2.2 branch
Suggested to use the Intel Fortran compiler 11.1 update 6 and later version.
There are some known issues with new Composer XE 2011 (ifort version 12.x.xxx). Please use the XE 2011 update 8 and future version, also apply the following patches in configuration file "Linux-x86-64-intel.sopt":
FCFLAGS2 = -I$(INTEL_INC) -O1 -xHost -heap-arrays 64 -fpp -free $(DFLAGS)
et_coupling.o: et_coupling.F
$(FC) -c $(FCFLAGS2) $<
qs_vxc_atom.o: qs_vxc_atom.F
$(FC) -c $(FCFLAGS2) $<
<end>
- DPD200161616
- DPD200172602
Comments
When I run this test cd cp2k/tests/QS
] ./../../exe/Linux-x86-64-intel/cp2k.sopt H2O-32.inp
I am getting *** 11:16:13 ERRORL2 in cp_fm_cholesky:cp_fm_cholesky_decompose processor ***
I am using ifort 11.1.069
[as845383@pauling QS]$ ldd /opt/cp2k/exe/Linux-x86-64-intel/cp2k.sopt
libmkl_intel_lp64.so => /opt/intel/mkl/10.2.4.032/lib/em64t/libmkl_intel_lp64.so (0x00002ae74e810000)
libmkl_sequential.so => /opt/intel/mkl/10.2.4.032/lib/em64t/libmkl_sequential.so (0x00002ae74ec0a000)
libmkl_core.so => /opt/intel/mkl/10.2.4.032/lib/em64t/libmkl_core.so (0x00002ae74f382000)
libm.so.6 => /lib64/libm.so.6 (0x0000003a1e400000)
libiomp5.so => /opt/intel/mkl/10.2.4.032/lib/em64t/libiomp5.so (0x00002ae74f75f000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003a1e800000)
libc.so.6 => /lib64/libc.so.6 (0x0000003a1dc00000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003a2be00000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003a1e000000)
/lib64/ld-linux-x86-64.so.2 (0x0000003a1d800000)
Hi, Anne
What version of CP2K you have used ? version 2.1.xxx is recommended to use Intel Fortran compiler 11.1 update 6 (version 11.1.072). Please let us know if you still have problems with that ifort verison.
I successfully compiled CP2K version 2.1.390 (Development Version) using l_cprof_p_11.1.073 on Suse-Linux-X64 11.3.
I found it necessary to list the FFTW library before the MKL libraries, as follows in the file Linux-x86-64-intel.sopt.
LIBS = -L$(INTEL_LIB) -lfftw3xf_intel -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
Thanks for your update, mecej4. Welocome to report any issue you find and share with us.
I got error in ifort v 12.0.2.137
/home/joonho/cp2k/makefiles/../lib/Linux-x86-64-intel/sopt/libcp2k_fft_lib.a(fftacml_lib.o): In function `fftacml3d_':
/home/joonho/cp2k/makefiles/../src/lib/fftacml_lib.F:(.text+0xbe0): undefined reference to `zfft3dx_'
/home/joonho/cp2k/makefiles/../src/lib/fftacml_lib.F:(.text+0xc50): undefined reference to `zfft3dx_'
Can you indicate me how to compile cp2k with libint? I always get segmentation errors at the stage where HFX_MEM_INFO would be printed out:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
cp2k.popt 0000000001321BCE Unknown Unknown Unknown
...
Usually, it does not happen with gfortran. Does ifort really not support ISO_C_BINDINGS?
Thanks!
I was able to compile cp2k with libint and calculating with hybrid functionals without getting seg faults. One simply has to remove -xHost from FCFLAGS. I'll try to find out which source file actually is responsible for the problem, therefore, it should be possible to optimize the rest of the program with -xHost put and apply FCFLAGS2 to the affected routine, module, source file.
It seems that ifort (e.g.11.1.072) doesn't support ISO_C_BINDINGS. Using the following setup in Linux-x86-64-intel.popt, I successfully compiled cp2k with libint for the hybrid functional calculation without segmental fault.
CC = cc
CPP =
FC = mpif90
LD = mpif90
AR = ar -r
DFLAGS = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -D__FFTW3 -D__LIBINT -D__HAS_NO_ISO_C_BINDING
CPPFLAGS =
INTEL_INC = /usr/apps/isv/intel/11.1.072/include
LIBINT_INC = $(HOME)/soft/libint-1.1.4/include
FFTW_INC = /usr/apps/free/fftw/3.2.2_i/include
FCFLAGS = $(DFLAGS) -I$(LIBINT_INC) -I$(INTEL_INC) -I$(FFTW_INC) -O2 -xW -heap-arrays 64 -funroll-loops -fpp -free
FCFLAGS2 = $(DFLAGS) -I$(LIBINT_INC) -I$(INTEL_INC) -O1 -xW -heap-arrays 64 -fpp -free
LDFLAGS = $(FCFLAGS) -I$(INTEL_INC)
FFTW_LIB = /usr/apps/free/fftw/3.2.2_i
INTEL_LIB = /usr/apps/isv/intel/11.1.072/mkl/lib/em64t
LIBINT = $(HOME)/soft/libint-1.1.4
LIBS =-L$(INTEL_LIB)/ -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
$(HOME)/soft/cp2k-2.1/tools/hfx_tools/libint_tools/libint_cpp_wrapper.o
$(LIBINT)/lib/libderiv.a
$(LIBINT)/lib/libint.a
-lstdc++
$(FFTW_LIB)/lib/libfftw3.a
OBJECTS_ARCHITECTURE = machine_intel.o
graphcon.o: graphcon.F
$(FC) -c $(FCFLAGS2) $<
qs_vxc_atom.o: qs_vxc_atom.F
$(FC) -c $(FCFLAGS2) $<
-------
The gcc and ifort are used for compiling the libint-1.1.4.
If want to use libint, please add/modify the following lines in “Linux-x86-64-intel.sopt”:
LIBINT_PATH= <your install path>/libint-1.1.4
LIBINT_LIB = $(LIBINT_LIB)/lib/libderiv.a $(LIBINT_LIB)/lib/libint.a -lstdc++
DFLAGS = -D__INTEL -D__FFTSG -D__FFTW3 -D__FFTMKL -D__LIBINT
LIBS = -L$(INTEL_LIB) -mkl $(LIBINT_LIB)
It works with Composer XE 2011 (aka 12.0) and later version.
There are some known issues found on Fortran Composer XE 2011 update 6 (or version 12.1.233) with latest CP2K 2.2 branch (using CP2K version 2.2.347 in my testing)
In summary :
1) Two source files 'et_coupling.F' and 'qs_vxc_atom.F' need to compiled with -O1 option. Please apply FCFLAGS2 patch to them.
2) One source file 'xc_pot_saop.F' need to compile with -xSSE2 option (instead of -xHost). Suggest to apply another FCFLAGS3 patch looks like:
FCFLAGS3 = -I$(INTEL_INC) -O2 -xSSE2 -heap-arrays 64 -fpp -free $(DFLAGS)
xc_pot_saop.o: xc_pot_saop.F
$(FC) -c $(FCFLAGS3) $<
Please report any other issues you have found. Thanks
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