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小木虫论坛-学术科研互动平台 » 计算模拟区 » 第一性原理 » QE(Pwscf) » PWscf 安装运行问题
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chenjfeng

新虫 (初入文坛)

[求助] PWscf 安装运行问题已有1人参与

各位虫友，我在集群node1上编译编译了pw.x 但运行不了出现如下情况

Checking atom-lsda...0 - <NO ERROR MESSAGE> : Could not convert index 1140850688 into a pointer
The index may be an incorrect argument.
Possible sources of this problem are a missing "include 'mpif.h'",
a misspelled MPI object (e.g., MPI_COM_WORLD instead of MPI_COMM_WORLD)
or a misspelled user variable for an MPI object (e.g.,
com instead of comm).
[0]  Aborting program !
[0] Aborting program!
FAILED with error condition!
Input: atom-lsda.in, Output: atom-lsda.out, Reference: atom-lsda.ref
Aborting

求解释，求解决……
如能顺利解决，愿奉金币……
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1楼2015-01-16 20:59:30
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liqizuiyang

木虫 (著名写手)
贴几个cpnfigure，楼主参考下：

1. 集群，LFS任务调度系统，intelmpi，FFTW-3.3.4，MKL，静态链接
export MPIF90=mpiifort
export F77=ifort
export F90=ifort
export FC=ifort

export CFLAGS=-O2
export FCFLAGS=-O2
export FFLAGS=-O2

export MKLDIR=$HOME/lib/mkl-13.0.080

./configure \
BLAS_LIBS="-Wl,--start-group $MKLDIR/libmkl_intel_lp64.a $MKLDIR/libmkl_sequential.a $MKLDIR/libmkl_core.a -Wl,--end-group" \
SCALAPACK_LIBS="-Wl,--start-group $MKLDIR/libmkl_scalapack_lp64.a $MKLDIR/libmkl_blacs_intelmpi_lp64.a -Wl,--end-group" \
FFT_LIBS="$HOME/lib/fftw-3.3.4/lib/libfftw3.a"


2. 天河1A，默认mpi，FFTW-3.3.4，MKL，静态链接
export MPIF90=mpif90
export F90=ifort
export F77=ifort
export FC=ifort

export CFLAGS=-O2
export FFLAGS=-O2
export FCFLAGS=-O2

export MKL_LIB_PATH=/opt/intel/composer_xe_2013.0.079/mkl/lib/intel64
export FFT_LIB_PATH=$HOME/lib/fftw-3.3.4/lib

./configure \
BLAS_LIBS="-Wl,--start-group \
$MKL_LIB_PATH/libmkl_intel_lp64.a \
$MKL_LIB_PATH/libmkl_sequential.a \
$MKL_LIB_PATH/libmkl_core.a \
-Wl,--end-group" \
SCALAPACK_LIBS="-Wl,--start-group \
$MKL_LIB_PATH/libmkl_scalapack_lp64.a \
$MKL_LIB_PATH/libmkl_blacs_intelmpi_lp64.a \
-Wl,--end-group" \
FFT_LIBS="$FFT_LIB_PATH/libfftw3.a"



3. 单节点，openmpi + MKL + FFTW，动态链接
export MPIF90=mpif90
export F90=ifort
export F77=ifort
export FC=ifort

export CFLAGS=-O2
export FCFLAGS=-O2
export FFLAGS=-O2

./configure FFT_LIBS="$HOME/code/fftw-3.3.4/lib/libfftw3.a"
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13楼2015-01-19 14:11:49
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普通回帖

KalaShayminS

铁杆木虫 (著名写手)

【答案】应助回帖

★
感谢参与，应助指数 +1
ljw4010: 金币+1, 谢谢交流！ 2015-01-18 21:06:02
是用mpi编译的并行版本吗？
这样可能是编译有问题。
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2楼2015-01-16 21:23:00
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516518

铜虫 (小有名气)
刚学不久，如楼上所言，好像是并行环境设置有问题
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3楼2015-01-17 05:19:48
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chenjfeng

新虫 (初入文坛)
引用回帖:
2楼: Originally posted by KalaShayminS at 2015-01-16 21:23:00
是用mpi编译的并行版本吗？
这样可能是编译有问题。

是并行版本

安装时，直接./configure, make没有成功。修改make.sys

修改前    SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
修改后    SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64

以下是make.sys 求指导……
***************************************************************

# make.sys.  Generated from make.sys.in by configure.

# compilation rules

.SUFFIXES :
.SUFFIXES : .o .c .f .f90

# most fortran compilers can directly preprocess c-like directives: use
#         $(MPIF90) $(F90FLAGS) -c $<
# if explicit preprocessing by the C preprocessor is needed, use:
#         $(CPP) $(CPPFLAGS) $< -o $*.F90
#        $(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
# remember the tabulator in the first column !!!

.f90.o:
        $(MPIF90) $(F90FLAGS) -c $<

# .f.o and .c.o: do not modify

.f.o:
        $(F77) $(FFLAGS) -c $<

.c.o:
        $(CC) $(CFLAGS)  -c $<



# topdir for linking espresso libs with plugins
TOPDIR = /public/home/cl_hqk/cjf/software/espresso-5.1.1

# DFLAGS  = precompilation options (possible arguments to -D and -U)
#           used by the C compiler and preprocessor
# FDFLAGS = as DFLAGS, for the f90 compiler
# See include/defs.h.README for a list of options and their meaning
# With the exception of IBM xlf, FDFLAGS = $(DFLAGS)
# For IBM xlf, FDFLAGS is the same as DFLAGS with separating commas

# MANUAL_DFLAGS  = additional precompilation option(s), if desired
#                  You may use this instead of tweaking DFLAGS and FDFLAGS
#                  BEWARE: will not work for IBM xlf! Manually edit FDFLAGS
MANUAL_DFLAGS  =
DFLAGS         =  -D__INTEL -D__FFTW -D__MPI -D__PARA -D__SCALAPACK $(MANUAL_DFLAGS)
FDFLAGS        = $(DFLAGS) $(MANUAL_DFLAGS)

# IFLAGS = how to locate directories where files to be included are
# In most cases, IFLAGS = -I../include

IFLAGS         = -I../include

# MOD_FLAGS = flag used by f90 compiler to locate modules
# Each Makefile defines the list of needed modules in MODFLAGS

MOD_FLAG      = -I

# Compilers: fortran-90, fortran-77, C
# If a parallel compilation is desired, MPIF90 should be a fortran-90
# compiler that produces executables for parallel execution using MPI
# (such as for instance mpif90, mpf90, mpxlf90,...);
# otherwise, an ordinary fortran-90 compiler (f90, g95, xlf90, ifort,...)
# If you have a parallel machine but no suitable candidate for MPIF90,
# try to specify the directory containing "mpif.h" in IFLAGS
# and to specify the location of MPI libraries in MPI_LIBS

MPIF90         = mpif90
#F90           = ifort
CC             = icc
F77            = ifort

# C preprocessor and preprocessing flags - for explicit preprocessing,
# if needed (see the compilation rules above)
# preprocessing flags must include DFLAGS and IFLAGS

CPP            = cpp
CPPFLAGS       = -P -C -traditional $(DFLAGS) $(IFLAGS)

# compiler flags: C, F90, F77
# C flags must include DFLAGS and IFLAGS
# F90 flags must include MODFLAGS, IFLAGS, and FDFLAGS with appropriate syntax

CFLAGS         = -O3 $(DFLAGS) $(IFLAGS)
F90FLAGS       = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS)
FFLAGS         = -O2 -assume byterecl -g -traceback

# compiler flags without optimization for fortran-77
# the latter is NEEDED to properly compile dlamch.f, used by lapack

FFLAGS_NOOPT   = -O0 -assume byterecl -g -traceback

# compiler flag needed by some compilers when the main is not fortran
# Currently used for Yambo

FFLAGS_NOMAIN   = -nofor_main

# Linker, linker-specific flags (if any)
# Typically LD coincides with F90 or MPIF90, LD_LIBS is empty

LD             = mpif90
LDFLAGS        = -static-intel
LD_LIBS        =

# External Libraries (if any) : blas, lapack, fft, MPI

# If you have nothing better, use the local copy :
# BLAS_LIBS = /your/path/to/espresso/BLAS/blas.a
# BLAS_LIBS_SWITCH = internal

BLAS_LIBS      =   -lmkl_intel_lp64  -lmkl_sequential -lmkl_core
BLAS_LIBS_SWITCH = external

# If you have nothing better, use the local copy :
# LAPACK_LIBS = /your/path/to/espresso/lapack-3.2/lapack.a
# LAPACK_LIBS_SWITCH = internal
# For IBM machines with essl (-D__ESSL): load essl BEFORE lapack !
# remember that LAPACK_LIBS precedes BLAS_LIBS in loading order

LAPACK_LIBS    =
LAPACK_LIBS_SWITCH = external

ELPA_LIBS_SWITCH = disabled
SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64

# nothing needed here if the the internal copy of FFTW is compiled
# (needs -D__FFTW in DFLAGS)

FFT_LIBS       =

# For parallel execution, the correct path to MPI libraries must
# be specified in MPI_LIBS (except for IBM if you use mpxlf)

MPI_LIBS       =

# IBM-specific: MASS libraries, if available and if -D__MASS is defined in FDFLAGS

MASS_LIBS      =

# ar command and flags - for most architectures: AR = ar, ARFLAGS = ruv

AR             = ar
ARFLAGS        = ruv

# ranlib command. If ranlib is not needed (it isn't in most cases) use
# RANLIB = echo

RANLIB         = ranlib

# all internal and external libraries - do not modify

FLIB_TARGETS   = all

LIBOBJS        = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
LIBS           = $(SCALAPACK_LIBS) $(LAPACK_LIBS) $(FFT_LIBS) $(BLAS_LIBS) $(MPI_LIBS) $(MASS_LIBS) $(LD_LIBS)

# wget or curl - useful to download from network
WGET = wget -O

# Install directory
PREFIX = $(INSTALLDIR)
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4楼2015-01-17 09:10:14
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KalaShayminS

铁杆木虫 (著名写手)

【答案】应助回帖

★
ljw4010: 金币+1, 谢谢交流！ 2015-01-18 21:06:15
你的MPI是什么MPI？是OpenMPI吗？这个不匹配会引起这个错误。
可以先去掉Scallapack的编译选项试试。
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5楼2015-01-17 09:47:46
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516518

铜虫 (小有名气)
如果并行安装成功，./configure时会自动识别的
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6楼2015-01-17 11:30:36
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chenjfeng

新虫 (初入文坛)
引用回帖:
5楼: Originally posted by KalaShayminS at 2015-01-17 09:47:46
你的MPI是什么MPI？是OpenMPI吗？这个不匹配会引起这个错误。
可以先去掉Scallapack的编译选项试试。

去掉Scallapack，不能顺利make

像我这种问题，应该是编译安装时的错误，还是运行时environment-variables 设置的问题呢？？
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7楼2015-01-18 16:02:22
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chenjfeng

新虫 (初入文坛)
引用回帖:
6楼: Originally posted by 516518 at 2015-01-17 11:30:36
如果并行安装成功，./configure时会自动识别的

./configure时，DFLAGS 显示是-D_MPI
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8楼2015-01-18 16:16:31
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516518

铜虫 (小有名气)
./configure时，如果并行设置成功应显示Parallel environment detected successfully，要不就是没设好，楼主装的好像是MPI，可以先测试一下，并行设置有没有问题
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9楼2015-01-18 16:57:19
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chenjfeng

新虫 (初入文坛)
引用回帖:
9楼: Originally posted by 516518 at 2015-01-18 16:57:19
./configure时，如果并行设置成功应显示Parallel environment detected successfully，要不就是没设好，楼主装的好像是MPI，可以先测试一下，并行设置有没有问题

显示 Parallel environment detected successfully，前面也说过直接make，会出现undefine opmpi…… 错误 根据网上搜索
修改前    SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64
修改后    SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64
做上面改动 顺利make 就是运行test里面的check…… 出现主题所提到的错误
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10楼2015-01-18 18:13:16
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