[gmx-users] installation with intel compilers
Erik Lindahl
lindahl at csb.stanford.edu
Mon Feb 2 18:07:01 CET 2004
Hi,
A couple of suggestions:
1. Skip the fortran compiler. You'll be using assembly loops on a P4
anyway, so it won't improve performance.
2. Compile FFTW with exactly the same compiler and exactly the same
flags instead of using the RPMs.
Cheers,
Erik
On Feb 2, 2004, at 5:48 PM, Sergio Modesto Vechi wrote:
> Hi All,
>
>
> I'm new on Gromacs and did my installation #1 on a P4 running linux
> redhat 9.0 with
> intel compilers 8.0. The installation with gnu compilers was fine but
> it was't true
> for intel ones.
>
> I installed the packages fftw-2.1.3-2 and fftw-devel-2.1.3-2, set
> paths and variables,
> then selected the compilers CC=icc and F77=ifort and set the flag
> CFLAGS="-O3 -axW -tpp7"
> (as I read on gmx-users list).
>
> After a "succesful" installation I ran the demo and got "Segmentation
> fault" error.
> I am sending the config.log for your reference. The installation with
> gnu compilers was fine.
>
> Does anyone have experience with this subject? I appreciate any help
> and suggestions.
>
> Thanks in advance,
>
>
> Sergio.
>
> -----------------------------------------------------------------------
> --
> Sergio Modesto Vechi, Post-Doctoral Researcher
> Department of Physics and Chemistry
> Faculty of Pharmaceutical Sciences of Ribeirao Preto
> University of Sao Paulo
> Brazil
> -----------------------------------------------------------------------
> --
>
> This file contains any messages produced by compilers while
> running configure, to aid debugging if configure makes a mistake.
>
> It was created by GROMACS configure 3.1.4, which was
> generated by GNU Autoconf 2.52. Invocation command line was
>
> $ ./configure
>
> ## ---------- ##
> ## Platform. ##
> ## ---------- ##
>
> hostname = arg.fq
> uname -m = i686
> uname -r = 2.4.20-8
> uname -s = Linux
> uname -v = #1 Thu Mar 13 17:54:28 EST 2003
>
> /usr/bin/uname -p = unknown
> /bin/uname -X = unknown
>
> /bin/arch = i686
> /usr/bin/arch -k = unknown
> /usr/convex/getsysinfo = unknown
> hostinfo = unknown
> /bin/machine = unknown
> /usr/bin/oslevel = unknown
> /bin/universe = unknown
>
> PATH =
> /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/
> usr/X11R6/bin:./:/home/smv/bin:/usr/local/Acrobat5/bin/:/opt/
> intel_cc_80/bin:/opt/intel_fc_80/bin:/opt/intel_idb_73/bin:/home/smv/
> bin:./:/home/smv/bin:/usr/local/Acrobat5/bin/:/opt/intel_cc_80/bin:/
> opt/intel_fc_80/bin:/opt/intel_idb_73/bin:./:/home/smv/bin:/usr/local/
> Acrobat5/bin/:/opt/intel_cc_80/bin:/opt/intel_fc_80/bin:/opt/
> intel_idb_73/bin:./:/home/smv/bin:/usr/local/Acrobat5/bin/:/opt/
> intel_cc_80/bin:/opt/intel_fc_80/bin:/opt/intel_idb_73/bin:/opt/
> intel_cc_80/bin:/opt/intel_fc_80/bin:/opt/intel_idb_73/bin:/opt/
> intel_cc_80/include:/opt/intel_cc_80/lib:/opt/intel_fc_80/include:/
> opt/intel_fc_80/lib
>
> ## ------------ ##
> ## Core tests. ##
> ## ------------ ##
>
> configure:1184: PATH=".;."; conftest.sh
> ./configure: line 1185: conftest.sh: command not found
> configure:1187: $? = 127
> configure:1227: checking build system type
> configure:1245: result: i686-pc-linux-gnu
> configure:1252: checking host system type
> configure:1266: result: i686-pc-linux-gnu
> configure:1285: checking for a BSD compatible install
> configure:1334: result: /usr/bin/install -c
> configure:1345: checking whether build environment is sane
> configure:1388: result: yes
> configure:1421: checking for awk
> configure:1436: found /usr/bin/awk
> configure:1444: result: awk
> configure:1454: checking whether make sets ${MAKE}
> configure:1474: result: yes
> configure:2005: checking for C compiler version
> configure:2008: icc --version </dev/null >&5
> 8.0
> configure:2011: $? = 0
> configure:2013: icc -v </dev/null >&5
> Version 8.0
> configure:2016: $? = 0
> configure:2018: icc -V </dev/null >&5
> Intel(R) C++ Compiler for 32-bit applications, Version 8.0 Build
> 20031016Z Package ID: l_cc_p_8.0.055
> Copyright (C) 1985-2003 Intel Corporation. All rights reserved.
> FOR NON-COMMERCIAL USE ONLY
>
> icc: Command line error: no files specified; for help type "icc -help"
> configure:2021: $? = 1
> configure:2041: checking for C compiler default output
> configure:2044: icc -O3 -axW -tpp7 conftest.c >&5
> configure(2029) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:2047: $? = 0
> configure:2076: result: a.out
> configure:2081: checking whether the C compiler works
> configure:2087: ./a.out
> configure:2090: $? = 0
> configure:2105: result: yes
> configure:2112: checking whether we are cross compiling
> configure:2114: result: no
> configure:2117: checking for executable suffix
> configure:2119: icc -o conftest -O3 -axW -tpp7 conftest.c >&5
> configure(2029) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:2122: $? = 0
> configure:2144: result:
> configure:2150: checking for object suffix
> configure:2168: icc -c -O3 -axW -tpp7 conftest.c >&5
> configure(2160) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:2171: $? = 0
> configure:2190: result: o
> configure:2194: checking whether we are using the GNU C compiler
> configure:2215: icc -c -O3 -axW -tpp7 conftest.c >&5
> configure(2204) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:2218: $? = 0
> configure:2221: test -s conftest.o
> configure:2224: $? = 0
> configure:2236: result: yes
> configure:2242: checking whether icc accepts -g
> configure:2260: icc -c -g conftest.c >&5
> configure:2263: $? = 0
> configure:2266: test -s conftest.o
> configure:2269: $? = 0
> configure:2279: result: yes
> configure:2306: icc -c -O3 -axW -tpp7 conftest.c >&5
> conftest.c(2): error: identifier "choke" is undefined
> choke me
> ^
>
> conftest.c(3): error: expected a ";"
>
> compilation aborted for conftest.c (code 2)
> configure:2309: $? = 2
> configure: failed program was:
> #ifndef __cplusplus
> choke me
> #endif
> configure:2415: checking for style of include used by make
> configure:2442: result: GNU
> configure:2448: checking dependency style of icc
> configure:2510: result: gcc3
> configure:4065: checking how to run the C preprocessor
> configure:4091: icc -E conftest.c
> configure:4097: $? = 0
> configure:4124: icc -E conftest.c
> configure(4121): catastrophic error: could not open source file
> "ac_nonexistent.h"
> #include <ac_nonexistent.h>
> ^
>
> configure:4130: $? = 4
> configure: failed program was:
> #line 4120 "configure"
> #include "confdefs.h"
> #include <ac_nonexistent.h>
> configure:4167: result: icc -E
> configure:4182: icc -E conftest.c
> configure:4188: $? = 0
> configure:4215: icc -E conftest.c
> configure(4212): catastrophic error: could not open source file
> "ac_nonexistent.h"
> #include <ac_nonexistent.h>
> ^
>
> configure:4221: $? = 4
> configure: failed program was:
> #line 4211 "configure"
> #include "confdefs.h"
> #include <ac_nonexistent.h>
> configure:4600: checking whether icc accepts -O6
> configure:4618: result: no
> configure:4626: checking whether icc accepts -O4
> configure:4644: result: no
> configure:4652: checking whether icc accepts -O3
> configure:4670: result: yes
> configure:4697: checking whether icc accepts -malign-double
> configure:4715: result: no
> configure:4963: checking whether icc accepts -funroll-all-loops
> configure:4981: result: no
> configure:5121: checking whether your compiler can handle assembly
> files (*.s)
> configure:5129: icc -c conftestasm.s
> configure:5132: $? = 0
> configure:5135: result: yes
> configure:5187: checking whether as fully supports intel syntax SSE &
> 3DNow
> configure:5199: icc -c conftest.s
> configure:5202: $? = 0
> configure:5204: result: yes
> configure:5379: checking for ident
> configure:5396: found /usr/bin/ident
> configure:5408: result: /usr/bin/ident
> configure:5418: checking whether the compiler supports ident
> configure:5426: icc -E -I/usr/local/include conftest.c
> configure:5432: $? = 0
> configure:5444: result: yes
> configure:5543: checking for ld used by GCC
> configure:5607: result: /usr/bin/ld
> configure:5616: checking if the linker (/usr/bin/ld) is GNU ld
> GNU ld version 2.13.90.0.18 20030206
> configure:5628: result: yes
> configure:5632: checking for /usr/bin/ld option to reload object files
> configure:5639: result: -r
> configure:5648: checking for BSD-compatible nm
> configure:5683: result: /usr/bin/nm -B
> configure:5687: checking whether ln -s works
> configure:5691: result: yes
> configure:5698: checking how to recognise dependant libraries
> configure:5886: result: file_magic ELF [0-9][0-9]*-bit [LM]SB (shared
> object|dynamic lib )
> configure:6025: checking for dlfcn.h
> configure:6035: icc -E -I/usr/local/include conftest.c
> configure:6041: $? = 0
> configure:6060: result: yes
> configure:6073: checking the maximum length of command line arguments
> configure:6121: result: 32768
> configure:6129: checking command to parse /usr/bin/nm -B output from
> icc object
> configure:6214: icc -c -O3 -axW -tpp7 -I/usr/local/include conftest.c
> >&5
> conftest.c(9) : (col. 11) remark: main has been targeted for automatic
> cpu dispatch.
> configure:6217: $? = 0
> configure:6221: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[
> ]\([ABCDGISTW][ABCDGISTW]*\)[ ][
> ]*\(\)\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2\3 \3/p' \> conftest.nm
> configure:6224: $? = 0
> configure:6276: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c conftstm.o >&5
> configure:6279: $? = 0
> configure:6317: result: ok
> configure:6321: checking for objdir
> configure:6336: result: .libs
> configure:6419: checking for ranlib
> configure:6434: found /usr/bin/ranlib
> configure:6443: result: ranlib
> configure:6493: checking for strip
> configure:6508: found /usr/bin/strip
> configure:6517: result: strip
> configure:6569: checking for file
> configure:6622: result: /usr/bin/file
> configure:6773: checking if icc static flag works
> conftest.c(1) : (col. 7) remark: main has been targeted for automatic
> cpu dispatch.
> configure:6796: result: yes
> configure:6810: checking if icc supports -fno-rtti -fno-exceptions
> configure:6837: result: yes
> configure:6852: checking for icc option to produce PIC
> configure:7043: result: -fPIC
> configure:7050: checking if icc PIC flag -fPIC works
> configure:7077: result: yes
> configure:7097: checking if icc PIC define -DPIC works
> configure:7124: result: yes
> configure:7136: checking if icc supports -c -o file.o
> configure:7177: result: yes
> configure:7202: checking whether the icc linker (/usr/bin/ld) supports
> shared libraries
> configure:7998: result: yes
> configure:8063: checking how to hardcode library paths into programs
> configure:8087: result: immediate
> configure:8101: checking whether stripping libraries is possible
> configure:8106: result: yes
> configure:8113: checking dynamic linker characteristics
> configure:8555: result: GNU/Linux ld.so
> configure:9188: checking if libtool supports shared libraries
> configure:9190: result: yes
> configure:9193: checking whether to build shared libraries
> configure:9214: result: no
> configure:9217: checking whether to build static libraries
> configure:9221: result: yes
> configure:9300: creating libtool
> configure:18141: checking whether ln -s works
> configure:18145: result: yes
> configure:18159: checking for special C compiler options needed for
> large files
> configure:18239: result: no
> configure:18245: checking for _FILE_OFFSET_BITS value needed for large
> files
> configure:18279: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(18260): error: shift count is too large
> int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
> ^
>
> configure(18260): error: shift count is too large
> int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
> ^
>
> configure(18261): error: shift count is too large
> && LARGE_OFF_T % 2147483647 == 1)
> ^
>
> configure(18261): error: shift count is too large
> && LARGE_OFF_T % 2147483647 == 1)
> ^
>
> compilation aborted for conftest.c (code 2)
> configure:18282: $? = 2
> configure: failed program was:
> #line 18253 "configure"
> #include "confdefs.h"
> #include <sys/types.h>
> /* Check that off_t can represent 2**63 - 1 correctly.
> We can't simply define LARGE_OFF_T to be 9223372036854775807,
> since some C++ compilers masquerading as C compilers
> incorrectly reject 9223372036854775807. */
> #define LARGE_OFF_T (((off_t) 1 << 62) - 1 + ((off_t) 1 << 62))
> int off_t_is_large[(LARGE_OFF_T % 2147483629 == 721
> && LARGE_OFF_T % 2147483647 == 1)
> ? 1 : -1];
> #ifdef F77_DUMMY_MAIN
> # ifdef __cplusplus
> extern "C"
> # endif
> int F77_DUMMY_MAIN() { return 1; }
> #endif
> int
> main ()
> {
>
> ;
> return 0;
> }
> configure:18324: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(18316) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:18327: $? = 0
> configure:18330: test -s conftest.o
> configure:18333: $? = 0
> configure:18344: result: 64
> configure:18354: checking for _LARGE_FILES value needed for large files
> configure:18388: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(18380) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:18391: $? = 0
> configure:18394: test -s conftest.o
> configure:18397: $? = 0
> configure:18453: result: no
> configure:18465: checking for _LARGEFILE_SOURCE value needed for large
> files
> configure:18491: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(18484): error: identifier "fseeko" is undefined
> return !fseeko;
> ^
>
> compilation aborted for conftest.c (code 2)
> configure:18494: $? = 2
> configure: failed program was:
> #line 18473 "configure"
> #include "confdefs.h"
> #include <stdio.h>
> #ifdef F77_DUMMY_MAIN
> # ifdef __cplusplus
> extern "C"
> # endif
> int F77_DUMMY_MAIN() { return 1; }
> #endif
> int
> main ()
> {
> return !fseeko;
> ;
> return 0;
> }
> configure:18528: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(18520) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:18531: $? = 0
> configure:18534: test -s conftest.o
> configure:18537: $? = 0
> configure:18548: result: 1
> configure:18562: checking for fseeko
> configure:18586: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(18578) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:18589: $? = 0
> configure:18592: test -s conftest
> configure:18595: $? = 0
> configure:18605: result: yes
> configure:18621: Using built-in math library with intel compiler
> configure:19255: checking for sfftw.h
> configure:19276: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(19268) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:19279: $? = 0
> configure:19282: test -s conftest.o
> configure:19285: $? = 0
> configure:19289: result: yes
> configure:19324: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(19316) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:19327: $? = 0
> configure:19330: test -s conftest.o
> configure:19333: $? = 0
> configure:19492: checking for main in -lsfftw
> configure:19518: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lsfftw >&5
> configure(19510) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:19521: $? = 0
> configure:19524: test -s conftest
> configure:19527: $? = 0
> configure:19538: result: yes
> configure:19967: checking for srfftw.h
> configure:19988: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(19980) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:19991: $? = 0
> configure:19994: test -s conftest.o
> configure:19997: $? = 0
> configure:19999: result: yes
> configure:20021: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lsrfftw -lsfftw >&5
> configure(20013) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:20024: $? = 0
> configure:20027: test -s conftest
> configure:20030: $? = 0
> configure:20913: checking for rpc/rpc.h
> configure:20923: icc -E -I/usr/local/include conftest.c
> configure:20929: $? = 0
> configure:20948: result: yes
> configure:20956: checking for xdr_float in -lnsl
> configure:20989: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lsrfftw -lsfftw >&5
> configure(20981) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:20992: $? = 0
> configure:20995: test -s conftest
> configure:20998: $? = 0
> configure:21009: result: yes
> configure:21040: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lsrfftw -lsfftw >&5
> configure(21032) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21043: $? = 0
> configure:21046: test -s conftest
> configure:21049: $? = 0
> configure:20913: checking for rpc/xdr.h
> configure:20923: icc -E -I/usr/local/include conftest.c
> configure:20929: $? = 0
> configure:20948: result: yes
> configure:20956: checking for xdr_float in -lnsl
> configure:21009: result: yes
> configure:21040: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(21032) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21043: $? = 0
> configure:21046: test -s conftest
> configure:21049: $? = 0
> configure:21071: checking for working memcmp
> configure:21122: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(21090) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21125: $? = 0
> configure:21127: ./conftest
> configure:21130: $? = 0
> configure:21142: result: yes
> configure:21146: checking return type of signal handlers
> configure:21180: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(21172) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21183: $? = 0
> configure:21186: test -s conftest.o
> configure:21189: $? = 0
> configure:21199: result: void
> configure:21209: checking for vprintf
> configure:21252: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(21236) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21255: $? = 0
> configure:21258: test -s conftest
> configure:21261: $? = 0
> configure:21271: result: yes
> configure:21278: checking for _doprnt
> configure:21321: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(21305) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> /tmp/iccdcNtV2.o(.text+0x52): In function `main.J':
> : undefined reference to `_doprnt'
> /tmp/iccdcNtV2.o(.text+0x73): In function `main.A':
> : undefined reference to `_doprnt'
> configure:21324: $? = 1
> configure: failed program was:
> #line 21284 "configure"
> #include "confdefs.h"
> /* System header to define __stub macros and hopefully few prototypes,
> which can conflict with char _doprnt (); below. */
> #include <assert.h>
> /* Override any gcc2 internal prototype to avoid an error. */
> #ifdef __cplusplus
> extern "C"
> #endif
> /* We use char because int might match the return type of a gcc2
> builtin and then its argument prototype would still apply. */
> char _doprnt ();
> char (*f) ();
>
> #ifdef F77_DUMMY_MAIN
> # ifdef __cplusplus
> extern "C"
> # endif
> int F77_DUMMY_MAIN() { return 1; }
> #endif
> int
> main ()
> {
> /* The GNU C library defines this for functions which it implements
> to always fail with ENOSYS. Some functions are actually named
> something starting with __ and the normal name is an alias. */
> #if defined (__stub__doprnt) || defined (__stub____doprnt)
> choke me
> #else
> f = _doprnt;
> #endif
>
> ;
> return 0;
> }
> configure:21340: result: no
> configure:21353: checking if malloc debugging is wanted
> configure:21374: result: no
> configure:21381: checking for strcasecmp
> configure:21424: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(21408) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21427: $? = 0
> configure:21430: test -s conftest
> configure:21433: $? = 0
> configure:21443: result: yes
> configure:21456: checking for strdup
> configure:21499: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(21483) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21502: $? = 0
> configure:21505: test -s conftest
> configure:21508: $? = 0
> configure:21518: result: yes
> configure:21530: checking for X
> configure:21745: result: libraries /usr/X11R6/lib, headers
> /usr/X11R6/include
> configure:21902: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw -L/usr/X11R6/lib -lX11 >&5
> configure(21894) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:21905: $? = 0
> configure:21908: test -s conftest
> configure:21911: $? = 0
> configure:22049: checking for gethostbyname
> configure:22092: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(22076) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22095: $? = 0
> configure:22098: test -s conftest
> configure:22101: $? = 0
> configure:22111: result: yes
> configure:22244: checking for connect
> configure:22287: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(22271) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22290: $? = 0
> configure:22293: test -s conftest
> configure:22296: $? = 0
> configure:22306: result: yes
> configure:22372: checking for remove
> configure:22415: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(22399) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22418: $? = 0
> configure:22421: test -s conftest
> configure:22424: $? = 0
> configure:22434: result: yes
> configure:22500: checking for shmat
> configure:22543: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(22527) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22546: $? = 0
> configure:22549: test -s conftest
> configure:22552: $? = 0
> configure:22562: result: yes
> configure:22637: checking for IceConnectionNumber in -lICE
> configure:22670: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> -L/usr/X11R6/lib conftest.c -lICE -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(22662) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22673: $? = 0
> configure:22676: test -s conftest
> configure:22679: $? = 0
> configure:22690: result: yes
> configure:22723: checking for Motif
> configure:22765: icc -c -O3 -axW -tpp7 -I/usr/X11R6/include
> -I/usr/local/include conftest.c >&5
> configure(22757) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22768: $? = 0
> configure:22771: test -s conftest.o
> configure:22774: $? = 0
> configure:22856: icc -o conftest -O3 -axW -tpp7 -I/usr/X11R6/include
> -I/usr/local/include -L/usr/X11R6/lib conftest.c -lSM -lICE -lXm
> -lXt -lX11 -lnsl -lnsl -lsrfftw -lsfftw >&5
> configure(22848) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22859: $? = 0
> configure:22862: test -s conftest
> configure:22865: $? = 0
> configure:22952: result: libraries in default path, headers in default
> path
> configure:22965: checking for libXext and libXp
> configure:22986: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> -I/usr/X11R6/include -L/usr/X11R6/lib conftest.c -lSM -lICE -lX11
> -lnsl -lnsl -lsrfftw -lsfftw -lXm -lXt -lXext -lXp >&5
> configure(22978) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:22989: $? = 0
> configure:22992: test -s conftest
> configure:22995: $? = 0
> configure:22997: result: yes
> configure:23110: checking for limits.h
> configure:23120: icc -E -I/usr/local/include conftest.c
> configure:23126: $? = 0
> configure:23145: result: yes
> configure:23110: checking for strings.h
> configure:23120: icc -E -I/usr/local/include conftest.c
> configure:23126: $? = 0
> configure:23145: result: yes
> configure:23110: checking for unistd.h
> configure:23120: icc -E -I/usr/local/include conftest.c
> configure:23126: $? = 0
> configure:23145: result: yes
> configure:23162: checking for unistd.h
> configure:23197: result: yes
> configure:23209: checking for icc option to accept ANSI C
> configure:23272: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(23254) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:23275: $? = 0
> configure:23278: test -s conftest.o
> configure:23281: $? = 0
> configure:23298: result: none needed
> configure:23306: checking for an ANSI C-conforming const
> configure:23376: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(23322) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:23379: $? = 0
> configure:23382: test -s conftest.o
> configure:23385: $? = 0
> configure:23395: result: yes
> configure:23405: checking for ANSI C header files
> configure:23419: icc -E -I/usr/local/include conftest.c
> configure:23425: $? = 0
> configure:23512: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -L/usr/X11R6/lib -lnsl -lnsl -lsrfftw -lsfftw -lXm -lXt
> -lSM -lICE -lXext -lXp -lX11 >&5
> configure(23499) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:23515: $? = 0
> configure:23517: ./conftest
> configure:23520: $? = 0
> configure:23533: result: yes
> configure:23549: checking for sys/types.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for sys/stat.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for stdlib.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for string.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for memory.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for strings.h
> configure:23580: result: yes
> configure:23549: checking for inttypes.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for stdint.h
> configure:23561: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23564: $? = 0
> configure:23567: test -s conftest.o
> configure:23570: $? = 0
> configure:23580: result: yes
> configure:23549: checking for unistd.h
> configure:23580: result: yes
> configure:23590: checking for size_t
> configure:23617: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(23640): warning #279: controlling expression is constant
> if ((size_t *) 0)
> ^
>
> configure(23639) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:23620: $? = 0
> configure:23623: test -s conftest.o
> configure:23626: $? = 0
> configure:23636: result: yes
> configure:23648: checking whether struct tm is in sys/time.h or time.h
> configure:23674: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure(23666) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:23677: $? = 0
> configure:23680: test -s conftest.o
> configure:23683: $? = 0
> configure:23693: result: time.h
> configure:23703: checking for uid_t in sys/types.h
> configure:23723: result: yes
> configure:23737: checking for inline
> configure:23754: icc -c -O3 -axW -tpp7 -I/usr/local/include
> conftest.c >&5
> configure:23757: $? = 0
> configure:23760: test -s conftest.o
> configure:23763: $? = 0
> configure:23774: result: inline
> configure:23792: checking if the C compiler supports inline assembly
> configure:23813: icc -o conftest -O3 -axW -tpp7 -I/usr/local/include
> conftest.c -L/usr/X11R6/lib -lnsl -lnsl -lsrfftw -lsfftw -lXm -lXt
> -lSM -lICE -lXext -lXp -lX11 >&5
> configure(23805) : (col. 1) remark: main has been targeted for
> automatic cpu dispatch.
> configure:23816: $? = 0
> configure:23819: test -s conftest
> configure:23822: $? = 0
> configure:23824: result: yes
> configure:24132: creating ./config.status
>
> ## ----------------------- ##
> ## Running config.status. ##
> ## ----------------------- ##
>
> This file was extended by config.status (GROMACS 3.1.4) 2.52, executed
> with
> CONFIG_FILES =
> CONFIG_HEADERS =
> CONFIG_LINKS =
> CONFIG_COMMANDS =
>> ./config.status
> on arg.fq
>
> config.status:24675: creating Makefile
> config.status:24675: creating src/Makefile
> config.status:24675: creating src/gmxlib/Makefile
> config.status:24675: creating include/Makefile
> config.status:24675: creating include/types/Makefile
> config.status:24675: creating src/mdlib/Makefile
> config.status:24675: creating src/kernel/Makefile
> config.status:24675: creating src/tools/Makefile
> config.status:24675: creating src/ngmx/Makefile
> config.status:24675: creating src/contrib/Makefile
> config.status:24675: creating scripts/Makefile
> config.status:24675: creating admin/Makefile
> config.status:24675: creating share/Makefile
> config.status:24675: creating share/tutor/Makefile
> config.status:24675: creating share/tutor/gmxdemo/Makefile
> config.status:24675: creating share/tutor/nmr1/Makefile
> config.status:24675: creating share/tutor/nmr2/Makefile
> config.status:24675: creating share/tutor/water/Makefile
> config.status:24675: creating share/tutor/speptide/Makefile
> config.status:24675: creating share/template/Makefile
> config.status:24675: creating share/top/Makefile
> config.status:24675: creating share/html/Makefile
> config.status:24675: creating share/html/images/Makefile
> config.status:24675: creating share/html/online/Makefile
> config.status:24675: creating man/Makefile
> config.status:24675: creating man/man1/Makefile
> config.status:24767: creating src/config.h
>
> ## ----------------- ##
> ## Cache variables. ##
> ## ----------------- ##
>
> ac_cv_build=i686-pc-linux-gnu
> ac_cv_build_alias=i686-pc-linux-gnu
> ac_cv_c_compiler_gnu=yes
> ac_cv_c_const=yes
> ac_cv_c_inline=inline
> ac_cv_env_CC_set=set
> ac_cv_env_CC_value=icc
> ac_cv_env_CFLAGS_set=set
> ac_cv_env_CFLAGS_value='-O3 -axW -tpp7'
> ac_cv_env_CPPFLAGS_set=
> ac_cv_env_CPPFLAGS_value=
> ac_cv_env_CPP_set=
> ac_cv_env_CPP_value=
> ac_cv_env_CXXCPP_set=
> ac_cv_env_CXXCPP_value=
> ac_cv_env_CXXFLAGS_set=
> ac_cv_env_CXXFLAGS_value=
> ac_cv_env_CXX_set=
> ac_cv_env_CXX_value=
> ac_cv_env_F77_set=set
> ac_cv_env_F77_value=ifort
> ac_cv_env_FFLAGS_set=
> ac_cv_env_FFLAGS_value=
> ac_cv_env_LDFLAGS_set=
> ac_cv_env_LDFLAGS_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_func__doprnt=no
> ac_cv_func_connect=yes
> ac_cv_func_fseeko=yes
> ac_cv_func_gethostbyname=yes
> ac_cv_func_memcmp_working=yes
> ac_cv_func_remove=yes
> ac_cv_func_shmat=yes
> ac_cv_func_strcasecmp=yes
> ac_cv_func_strdup=yes
> ac_cv_func_vprintf=yes
> ac_cv_have_x='have_x=yes ac_x_includes=/usr/X11R6/include
> ac_x_libraries=/usr/X11R6/lib'
> ac_cv_header_dlfcn_h=yes
> ac_cv_header_inttypes_h=yes
> ac_cv_header_limits_h=yes
> ac_cv_header_memory_h=yes
> ac_cv_header_rpc_rpc_h=yes
> ac_cv_header_rpc_xdr_h=yes
> ac_cv_header_stdc=yes
> ac_cv_header_stdint_h=yes
> ac_cv_header_stdlib_h=yes
> ac_cv_header_string_h=yes
> ac_cv_header_strings_h=yes
> ac_cv_header_sys_stat_h=yes
> ac_cv_header_sys_types_h=yes
> ac_cv_header_unistd_h=yes
> ac_cv_host=i686-pc-linux-gnu
> ac_cv_host_alias=i686-pc-linux-gnu
> ac_cv_lib_ICE_IceConnectionNumber=yes
> ac_cv_lib_nsl_xdr_float=yes
> ac_cv_lib_sfftw___main=yes
> ac_cv_motif_includes=
> ac_cv_motif_libraries=
> ac_cv_objext=o
> ac_cv_path_IDENT=/usr/bin/ident
> ac_cv_path_install='/usr/bin/install -c'
> ac_cv_prog_AWK=awk
> ac_cv_prog_CPP='icc -E'
> ac_cv_prog_ac_ct_RANLIB=ranlib
> ac_cv_prog_ac_ct_STRIP=strip
> ac_cv_prog_cc_g=yes
> ac_cv_prog_cc_stdc=
> ac_cv_prog_make_make_set=yes
> ac_cv_struct_tm=time.h
> ac_cv_sys_file_offset_bits=64
> ac_cv_sys_large_files=no
> ac_cv_sys_largefile_CC=no
> ac_cv_sys_largefile_source=1
> ac_cv_type_signal=void
> ac_cv_type_size_t=yes
> ac_cv_type_uid_t=yes
> am_cv_CC_dependencies_compiler_type=gcc3
> lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB
> (shared object|dynamic lib )'
> lt_cv_file_magic_cmd='$MAGIC_CMD'
> lt_cv_file_magic_test_file='/lib/libc.so.6 /lib/libc-2.3.2.so'
> lt_cv_ld_reload_flag=-r
> lt_cv_objdir=.libs
> lt_cv_path_LD=/usr/bin/ld
> lt_cv_path_MAGIC_CMD=/usr/bin/file
> lt_cv_path_NM='/usr/bin/nm -B'
> lt_cv_prog_compiler_c_o=yes
> lt_cv_prog_compiler_rtti_exceptions=yes
> lt_cv_prog_gnu_ld=yes
> lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[
> ]\([ABCDGISTW][ABCDGISTW]*\)[ ][
> ]*\(\)\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2\3 \3/p'\'''
> lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^
> ]*\) $/ {\"\1\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\)
> \([^ ]*\)$/ {"\2", (lt_ptr) \&\2},/p'\'''
> lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern
> int \1;/p'\'''
> lt_cv_sys_max_cmd_len=32768
> lt_lt_cv_prog_compiler_c_o='"yes"'
> lt_lt_cv_sys_global_symbol_pipe='"sed -n -e '\''s/^.*[
> ]\\([ABCDGISTW][ABCDGISTW]*\\)[ ][
> ]*\\(\\)\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2\\3 \\3/p'\''"'
> lt_lt_cv_sys_global_symbol_to_c_name_address='"sed -n -e '\''s/^:
> \\([^ ]*\\) \$/ {\\\"\\1\\\", (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST]
> \\([^ ]*\\) \\([^ ]*\\)\$/ {\"\\2\", (lt_ptr) \\&\\2},/p'\''"'
> lt_lt_cv_sys_global_symbol_to_cdecl='"sed -n -e '\''s/^. .*
> \\(.*\\)\$/extern int \\1;/p'\''"'
>
> ## ------------ ##
> ## confdefs.h. ##
> ## ------------ ##
>
> #define PACKAGE "gromacs"
> #define VERSION "3.1.4"
> #define SOFTWARE_SQRT
> #define USE_X86_SSE_AND_3DNOW
> #define HAVE_IDENT
> #define HAVE_DLFCN_H 1
> #define _FILE_OFFSET_BITS 64
> #define _LARGEFILE_SOURCE 1
> #define HAVE_FSEEKO 1
> #define HAVE_LIBSFFTW 1
> #define FFTW_NAME_SFFTW
> #define HAVE_RPC_RPC_H 1
> #define HAVE_LIBNSL 1
> #define HAVE_RPC_XDR_H 1
> #define HAVE_LIBNSL 1
> #define RETSIGTYPE void
> #define HAVE_VPRINTF 1
> #define HAVE_STRCASECMP 1
> #define HAVE_STRDUP 1
> #define HAVE_MOTIF
> #define HAVE_LIMITS_H 1
> #define HAVE_STRINGS_H 1
> #define HAVE_UNISTD_H 1
> #define HAVE_UNISTD_H 1
> #define STDC_HEADERS 1
> #define HAVE_SYS_TYPES_H 1
> #define HAVE_SYS_STAT_H 1
> #define HAVE_STDLIB_H 1
> #define HAVE_STRING_H 1
> #define HAVE_MEMORY_H 1
> #define HAVE_STRINGS_H 1
> #define HAVE_INTTYPES_H 1
> #define HAVE_STDINT_H 1
> #define HAVE_UNISTD_H 1
> #define USE_X86TRUNC
>
>
> configure: exit 0
>
> ## ----------------------- ##
> ## Running config.status. ##
> ## ----------------------- ##
>
> This file was extended by config.status (GROMACS 3.1.4) 2.52, executed
> with
> CONFIG_FILES =
> CONFIG_HEADERS = src/config.h
> CONFIG_LINKS =
> CONFIG_COMMANDS =
>> ./config.status
> on arg.fq
>
> config.status:24767: creating src/config.h
> config.status:24908: src/config.h is unchanged
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