AMBER Archive (2009)

Subject: RE: [AMBER] Amber10, Serial compilation with ifort

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jul 12 2009 - 16:41:07 CDT

Hi Aldo,

This is not a problem with AMBER per se but with your compiler / environment. I suspect one of two things, the second one being the most likely:

1) The machine you are running on has a limit on the length of time / amount of memory a job can use. The compilation is exceeding this and you are getting killed. There is not much that can be done about this short of modifying these limits - speak to your admin and see if they have such limits etc. Worst case you could edit $AMBERHOME/src/sander/depend file and for nmr.f change FOPTFLAG to FFLAG to stop optimization of this file which will reduce compilation time and memory usage. You may also need to edit the top of nmr.f and remove the compile=optimized line.

2) This is a bug in the ifort 10.1 compiler. Can you try a new version of the compiler? Check the Intel website and see if there is a new point release for v10.1.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Aldo Humberto Romero
> Sent: Sunday, July 12, 2009 1:58 PM
> To: amber_at_ambermd.org
> Subject: [AMBER] Amber10, Serial compilation with ifort
>
> I have been trying to compile amber10 with ifort 101 unsuccessfully.
> AmberTools did compile quite smooth but amber10 stops with the
> message
>
>
> cpp -traditional -P -DBINTRAJ nmr.f > _nmr.f
> ifort -c -w95 -vec_report0 -mp1 -ip -O3 -axNP -FR -o nmr.o _nmr.f
> _nmr.f(1240): (col. 12) remark: nmr_mp_getnat_ has been targeted for
> automatic cpu dispatch.
> _nmr.f(8786): (col. 12) remark: nmr_mp_r6drv_ has been targeted for
> automatic cpu dispatch.
> _nmr.f(3229): (col. 12) remark: nmr_mp_nmrcms_ has been targeted for
> automatic cpu dispatch.
> _nmr.f(289): (col. 12) remark: nmr_mp_at2res_ has been targeted for
> automatic cpu dispatch.
> _nmr.f(575): (col. 12) remark: nmr_mp_commass_ has been targeted for
> automatic cpu dispatch.
> _nmr.f(502): (col. 12) remark: nmr_mp_chklin_ has been targeted for
> automatic cpu dispatch.
> ifort: error #10106: Fatal error in /opt/intel/fc/10.1.018/bin/fortcom,
> terminated by kill signal
> compilation aborted for _nmr.f (code 1)
> make[1]: *** [nmr.o] Error 1
> make[1]: se sale del directorio
> `/home/aldo/CLASSICAL_MD/Amber/amber10/src/sander'
> make: *** [serial] Error 2
>
>
> I am not sure if the problem is the compiler or there is something
> missing during the configure procedure.
>
> Any comments/help will be greatly appreciate it
>
> regards
>
>
> --
>
> Prof. Aldo Humberto Romero
> CINVESTAV-Unidad Queretaro
> Libramiento Norponiente 2000
> CP 76230, Queretaro, QRO, Mexico
> tel: 442 211 9909
> fax: 442 211 9938
>
> email: aromero_at_qro.cinvestav.mx
> aldorome_at_gmail.com
> www: qro.cinvestav.mx/~aromero
>
>
> _______________________________________________
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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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