[AMBER] xray_interface.f verified to work with PGI7.1-1

From: Rathbone, Dan L <d.l.rathbone.aston.ac.uk>
Date: Thu, 18 Nov 2010 14:52:51 +0000

Dear forum members
A colleague of mine is attempting to install Amber 11 onto an elderly Cray system and has run into the previously-documented error associated with xray_interface.f. He has tried the suggested fixes but to no avail. He is of the opinion that if he could obtain a copy of the file "xray_interface.f" from a working Amber 11 setup verified to work with PGI7.1-1 then he could carry on.

Is there anyone who could send me a copy of the file "xray_interface.f" verified to work with PGI7.1-1?

His message is appended to this email.

Thanks in advance.

Dan Rathbone

________________________________
Dr Dan Rathbone
School of Life and Health Sciences
Aston University
Aston Triangle
Birmingham
UK
________________________________



> Hi Dan,

>

> after a few attempts I have managed to build parallel version of

> AmberTools and started building Amber 11, until I came across this PGI

> (Fortlan90 compiler bug) this is how I found it.

> Currently Loaded Modulefiles:

> 1) pgi/7.1-1 2) mpich/mpich-pgi711

>

> This is the error.

>

> mpif90 -c -O1 -Mfree -o xray_globals.o _xray_globals.f cpp

> -traditional -P -DMPI xray_utils.f > _xray_utils.f mpif90 -c -O1

> -Mfree -o xray_utils.o _xray_utils.f

> PGF90-S-0000-Internal compiler error. size_ast_of: unexpected ast type

> 4 (_xray_utils.f: 567)

> 0 inform, 0 warnings, 1 severes, 0 fatal for write_header

> make[1]: *** [xray_utils.o] Error 2

> make[1]: Leaving directory `/data/apps/pgi64/amber_new/amber11/src/sander'

> make: *** [parallel] Error 2

>

> Building serial version produces the same error.

>

> I have found that the error is known to amber developers since January

> of 2009 it's in sander directory in file xray_interface.f here is the

> snippet: where is starts.

>

> ! GMS: Fix for pgf90 compiler

> character(len=4) :: this_residue_chainid

> ! begin

>

> and further down.

>

>

> ! GMS: Fix for pgf90 compiler

> this_residue_chainid = residue_chainid(ires)

>

> write(unit,'(A6,I5,1X,A4,A1,A3,1X,A1,I4,A1,3X,3F8.3,2F6.2,6X,2A4)')&

> merge('ATOM

> ','HETATM',any(resName==standard_pdb_residues)), &

> iatom,name,atom_altloc(iatom)(1:1), &

> resName,residue_chainid(ires)(1:1), &

> residue_number(ires),residue_icode(ires)(1:1), &

> coordinate(1:3,iatom), &

> atom_occupancy(iatom), &

> atom_bfactor(iatom), &

> ! GMS: Fix for pgf90 compiler

> !merge(residue_chainid(ires),' ',pdb_use_segid), &

> merge(this_residue_chainid,' ',pdb_use_segid), &

> atom_element(iatom)

> Looking at forum pages

> It appears that the problem was solved through this changes above, but

> I am getting the same error as if fix was not there My Fortran is non

> existent. I was going to suggest that if you purchase the licence and

> support , then perhaps you might ask for xray_interface.f file from

> amber guys (it's in a sander source) which would have all the correct

> fixes for PGI7.1-1. Then I believe I can build it.
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Received on Thu Nov 18 2010 - 07:00:04 PST
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