Thank you very much for all kind supports!
Dear Mengjuei,
I updated the compiler to the latest version available, which was 11.1 update 6 and the make completed!!
Thanks a lot!
However, as I tried to make test, I got another error,,,
----------------------------------------------------------------------------------------------------------
[amber/amber10/test] kenske% make -f Makefile_at test
( cd nab; make test )
=====================================================
Running test to make dna duplex:
/bin/sh: line 1: 1594 Segmentation fault ./duplex < duplex.in
make[1]: *** [duplex_test] Error 139
make: *** [test.nab] Error 2
----------------------------------------------------------------------------------------------------------
Dear Dr. Case,
I tried gcc first and did not work so I switched to icc..
As I try to do it again, after './configure_at gcc' I get the following messages.
____________________________________________________________
[:~/apps/amber10/src] kenske% make -f Makefile_at
mkdir /Users/kenske/apps/amber10/bin /Users/kenske/apps/amber10/lib /Users/kenske/apps/amber10/include
mkdir: /Users/kenske/apps/amber10/bin: File exists
mkdir: /Users/kenske/apps/amber10/lib: File exists
mkdir: /Users/kenske/apps/amber10/include: File exists
make: [install] Error 1 (ignored)
(cd ucpp-1.3 && make install )
Makefile:35: warning: overriding commands for target `.c.o'
../config.h:99: warning: ignoring old commands for target `.c.o'
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE mem.c
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE nhash.c
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE cpp.c
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE lexer.c
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE assert.c
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE macro.c
gcc -c -m32 -DBINTRAJ -DSTAND_ALONE eval.c
gcc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
ld: warning: in mem.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in nhash.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in cpp.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in lexer.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in assert.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in macro.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in eval.o, file was built for i386 which is not the architecture being linked (x86_64)
Undefined symbols:
"_main", referenced from:
start in crt1.10.6.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [ucpp] Error 1
make: *** [install] Error 2
--------------------------------------------------------------------------------------------------------
Erik,
Thank you very much for your extremely detailed instruction!
I have Amber10 and AmberTools1.2, so my procedure might be little different, right?
I have Xtools3.2.2 but my gcc seems to be little old(4.2.1).
I will try to update gcc and see if it works.
kenske
On 2010/05/20, at 17:26, Mengjuei Hsieh wrote:
> On Wed, May 19, 2010 at 10:07 PM, Kensuke Nakamura
> <kensuke-nm.is.naist.jp> wrote:
>> amber.c(535) (col. 1): internal error: 0_1428
>> compilation aborted for amber.c (code 4)
>
> Hi Kensuke,
>
> When you see an internal error from an Intel compiler, you can safely
> bet that's a compiler problem. Judging from the forum post
> http://software.intel.com/en-us/forums/showthread.php?t=68863, I think
> you can try to upgrade to a later compiler version 11.1 update 3 and
> see if that helps.
> --
> Mengjuei
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
Kensuke Nakamura
Nara Institute of Science and Technology
Graduate School of Information Science
8916-5 Takayama, Ikoma, Nara 630-0101
JAPAN
TEL: +81-743-72-5257 (Fax:5258)
E-mail: kensuke-nm.is.naist.jp
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Received on Thu May 20 2010 - 18:00:03 PDT
