Dear All,
I have one problem to install Amber11+AmberTools1.4 on a linux
cluster with a parallel version.
I do not have big problems to install serial version.
In the serial version, I install Tools first.
If I only use "./configure intel"
I have error messages like the following:
libtool: compile unable to infer tagged configuration
When I use the command "./configure -nobintraj intel", it works fine
for both AmberTools and Amber compilation.
My ifort version is
ifort (IFORT) 12.1.5 20120612
Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
After "make clean" command for both Tools and Amber,
go back to AmberTools/src directory,
./configure -mpi intel
I have following error messages:
Configuring Parallel NetCDF; (may be time-consuming)
Error: parallel NetCDF configure returned 77
Parallel NetCDF configure failed! Check the pnetcdf/config.log file.
Continuing but parallel NetCDF will be skipped.
Configuring NetCDF; (may be time-consuming)
NetCDF configure succeeded.
Configuring fftw-2.1.5; (may be time-consuming)
Error: fftw configure returned 1
fftw configure failed! Check the fftw2_config.log file.
Any help? I read the log file and they are listed below:
pnetcdf/config.log
_________________________________________________
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by configure, which was
generated by GNU Autoconf 2.61. Invocation command line was
$ ./configure
--prefix=/gscratch/pfaendtner/shaohui/amber11/AmberTools/src/pnetcdf
--disable-cxx --disable-fortran
## --------- ##
## Platform. ##
## --------- ##
hostname = login2.hyak.local
uname -m = x86_64
uname -r = 2.6.18-308.8.1.el5
uname -s = Linux
uname -v = #1 SMP Fri May 4 16:43:02 EDT 2012
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = x86_64
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
## ----------- ##
## Core tests. ##
## ----------- ##
configure:1734: checking for top-level source-directory
configure:1737: result:
/gscratch/pfaendtner/shaohui/amber11/AmberTools/src/pnetcdf
configure:1852: checking for gcc
configure:1879: result: mpicc
configure:2117: checking for C compiler version
configure:2124: mpicc --version >&5
icc (ICC) 11.1 20090827
Copyright (C) 1985-2009 Intel Corporation. All rights reserved.
configure:2127: $? = 0
configure:2134: mpicc -v >&5
Version 11.1
configure:2137: $? = 0
configure:2144: mpicc -V >&5
Intel(R) C Intel(R) 64 Compiler Professional for applications running
on Intel(R) 64, Version 11.1 Build 20090827 Package ID:
l_cproc_p_11.1.056
Copyright (C) 1985-2009 Intel Corporation. All rights reserved.
configure:2147: $? = 0
configure:2170: checking for C compiler default output file name
configure:2197: mpicc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-DNDEBUG conftest.c >&5
ld: cannot find -lnuma
configure:2200: $? = 1
configure:2238: result:
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME ""
| #define PACKAGE_TARNAME ""
| #define PACKAGE_VERSION ""
| #define PACKAGE_STRING ""
| #define PACKAGE_BUGREPORT ""
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:2245: error: C compiler cannot create executables
See `config.log' for more details.
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_env_CC_set=set
ac_cv_env_CC_value=mpicc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value=' -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE'
ac_cv_env_CPPFLAGS_set=set
ac_cv_env_CPPFLAGS_value=-DNDEBUG
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_YACC_set=
ac_cv_env_YACC_value=
ac_cv_env_YFLAGS_set=
ac_cv_env_YFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_prog_ac_ct_CC=mpicc
## ----------------- ##
## Output variables. ##
## ----------------- ##
ALLOCA=''
AR=''
ARFLAGS=''
CC='mpicc'
CC_MAKEDEPEND=''
CFLAGS=' -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE'
COMPILE_F=''
CPP=''
CPPFLAGS='-DNDEBUG'
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
FC='/sw/intel/Compiler/11.1/056/bin/intel64/ifort'
FFLAGS=''
FLIBS=''
FPP=''
FPPFLAGS=''
GREP=''
INSTALL_DATA=''
INSTALL_PROGRAM=''
INSTALL_SCRIPT=''
LDFLAGS=''
LEX=''
LEXLIB=''
LEX_OUTPUT_ROOT=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
M4=''
M4FLAGS=''
MAKEWHATIS_CMD=''
MATHLIB=''
MPICC=''
MPIF77=''
NM=''
NMFLAGS=''
OBJEXT=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
RANLIB=''
SHELL='/bin/sh'
SRCDIR='/gscratch/pfaendtner/shaohui/amber11/AmberTools/src/pnetcdf'
WHATIS=''
YACC=''
YFLAGS=''
ac_ct_CC='mpicc'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE}'
dvidir='${docdir}'
exec_prefix='NONE'
has_fortran=''
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/gscratch/pfaendtner/shaohui/amber11/AmberTools/src/pnetcdf'
prog=''
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
#define PACKAGE_NAME ""
#define PACKAGE_TARNAME ""
#define PACKAGE_VERSION ""
#define PACKAGE_STRING ""
#define PACKAGE_BUGREPORT ""
configure: exit 77
__________________________________________
For fftw, I think the problem is that the compiler couldn't find mpi
library for --enable-mpi.
However, I am really not sure what I can do for the pnetcdf problem.
Thanks a lot.
Cheers,
Shaohui
--
Dr. Shaohui Zheng
------------------------------------
Stay hungry and stay foolish.
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Received on Thu Aug 23 2012 - 17:30:04 PDT
