AMBER Archive (2004)

Subject: (long) Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem)

From: Tru Huynh (tru_at_pasteur.fr)
Date: Thu Dec 02 2004 - 14:00:17 CST

On Wed, Dec 01, 2004 at 09:44:12AM -0800, David A. Case wrote:
>
> We don't have any opteron machines here; it would be great if some list reader
> who does have such a machine could see if they could reprodcue the "strange
> behavior" cited:
>
...

Hi,

just my .02 cents. I have recompiled amber8 on IA32 with the intel7 and PGI-5.2-4
and on x86_64 with only PGI-5.2-4 and leap with gcc.

bottom line, buggy PGI C compiler :( on both 32 and 64 bits

Tru

0) procedure
------------
. tar xzvf /Bis/shared/centos-3/amber8-common/amber8.tgz
. cd amber8
. patch -p0 -N -r patch_rejects < /Bis/shared/centos-3/amber8-common/bugfix.all
 
patching file src/leap/src/leap/unitio.c
patching file src/configure
patching file src/antechamber/pdb.c
patching file src/pbsa/pb_force.f
Hunk #1 succeeded at 3505 (offset -3 lines).
patching file src/configure
Hunk #1 succeeded at 728 (offset 13 lines).
patching file src/antechamber/am1bcc.c
...
patching file dat/leap/parm/glycam04EP.dat
patching file src/sander/rdparm.f
Hunk #1 FAILED at 66.
1 out of 1 hunk FAILED -- saving rejects to file patch_rejects
patching file src/pbsa/rdparm.f
Hunk #1 FAILED at 51.
1 out of 1 hunk FAILED -- saving rejects to file patch_rejects
patching file src/anal/locmem.f

:( patch_reject available on request (no need to spam the list)

. setenv AMBERHOME `pwd`
. setenv PATH $AMBERHOME/exe:$PATH
. cd src
. ./configure {ifc7, pgf90}
. cd src/leap && make install
. rehash
. tleap -f /Bis/scratch/tru/input.tleap

/Bis/scratch/tru/input.tleap:
---------------------------
source leaprc.ff94
a = ACE
solvatebox a TIP3PBOX 10
quit

1) IA32+intel7.1: -> OK
-----------------
[tru_at_xiii src]$ tleap -f /Bis/scratch/tru/input.tleap
-I: Adding /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/prep to search path.
-I: Adding /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib to search path.
-I: Adding /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/parm to search path.
-I: Adding /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/cmd to search path.
-f: Source /Bis/scratch/tru/input.tleap.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Bis/scratch/tru/input.tleap
----- Source: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/cmd/leaprc.ff94
----- Source of /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/parm/parm94.dat
Loading library: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib/all_nucleic94.lib
Loading library: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib/all_amino94.lib
Loading library: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib/all_aminoct94.lib
Loading library: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib/all_aminont94.lib
Loading library: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib/ions94.lib
Loading library: /Bis/shared/centos-3/amber8_intel-7.1/dat/leap/lib/solvents.lib
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 28.370 27.815 angstroms.
  Volume: 22814.792 A^3
  Total mass 8402.468 amu, Density 0.612 g/cc
  Added 464 residues.
        Quit

2) IA32/PGI-5.2-4 -> WRONG
-----------------
[tru_at_xiii ~/amber8_pgi-5.2-4]$ tleap -f /Bis/scratch/tru/input.tleap
-I: Adding /home/tru/amber8_pgi-5.2-4/dat/leap/prep to search path.
-I: Adding /home/tru/amber8_pgi-5.2-4/dat/leap/lib to search path.
-I: Adding /home/tru/amber8_pgi-5.2-4/dat/leap/parm to search path.
-I: Adding /home/tru/amber8_pgi-5.2-4/dat/leap/cmd to search path.
-f: Source /Bis/scratch/tru/input.tleap.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Bis/scratch/tru/input.tleap
----- Source: /home/tru/amber8_pgi-5.2-4/dat/leap/cmd/leaprc.ff94
----- Source of /home/tru/amber8_pgi-5.2-4/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /home/tru/amber8_pgi-5.2-4/dat/leap/parm/parm94.dat
Loading library: /home/tru/amber8_pgi-5.2-4/dat/leap/lib/all_nucleic94.lib
Loading library: /home/tru/amber8_pgi-5.2-4/dat/leap/lib/all_amino94.lib
Loading library: /home/tru/amber8_pgi-5.2-4/dat/leap/lib/all_aminoct94.lib
Loading library: /home/tru/amber8_pgi-5.2-4/dat/leap/lib/all_aminont94.lib
Loading library: /home/tru/amber8_pgi-5.2-4/dat/leap/lib/ions94.lib
Loading library: /home/tru/amber8_pgi-5.2-4/dat/leap/lib/solvents.lib
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 22.002 22.520 angstroms.
  Volume: 14325.344 A^3
  Total mass 20220.964 amu, Density 2.344 g/cc
  Added 1120 residues.
        Quit

3) IA32/gcc -> OK
-----------------
. cd src/leap
. make install CC=gcc LOADCC=gcc CFLAGS=''
. setenv PATH $AMBERHOME/exe:$PATH
. rehash

[tru_at_xiii leap]$ tleap -f /Bis/scratch/tru/input.tleap
-I: Adding /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/prep to search path.
-I: Adding /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib to search path.
-I: Adding /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/parm to search path.
-I: Adding /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/cmd to search path.
-f: Source /Bis/scratch/tru/input.tleap.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Bis/scratch/tru/input.tleap
----- Source: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/cmd/leaprc.ff94
----- Source of /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/parm/parm94.dat
Loading library: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib/all_nucleic94.lib
Loading library: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib/all_amino94.lib
Loading library: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib/all_aminoct94.lib
Loading library: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib/all_aminont94.lib
Loading library: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib/ions94.lib
Loading library: /home/tru/amber8_pgi-5.2-4+gcc/dat/leap/lib/solvents.lib
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 28.370 27.815 angstroms.
  Volume: 22814.792 A^3
  Total mass 8402.468 amu, Density 0.612 g/cc
  Added 464 residues.
        Quit

4) x86_64/PGI-5.2-4 -> WRONG
----------------------------
[tru_at_snivel ~]$ tleap -f /Bis/scratch/tru/input.tleap
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/prep to search path.
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib to search path.
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/parm to search path.
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/cmd to search path.
-f: Source /Bis/scratch/tru/input.tleap.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Bis/scratch/tru/input.tleap
----- Source: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/cmd/leaprc.ff94
----- Source of /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/parm/parm94.dat
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib/all_nucleic94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib/all_amino94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib/all_aminoct94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib/all_aminont94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib/ions94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4/dat/leap/lib/solvents.lib
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 22.002 22.520 angstroms.
  Volume: 14325.344 A^3
  Total mass 20220.964 amu, Density 2.344 g/cc
  Added 1120 residues.
        Quit

5) x86_64/gcc: -> OK
-------------
. cd src/leap && make install CC=gcc LOADCC=gcc
[tru_at_snivel leap]$ tleap -f /Bis/scratch/tru/input.tleap
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/prep to search path.
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib to search path.
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/parm to search path.
-I: Adding /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/cmd to search path.
-f: Source /Bis/scratch/tru/input.tleap.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /Bis/scratch/tru/input.tleap
----- Source: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/cmd/leaprc.ff94
----- Source of /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/parm/parm94.dat
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib/all_nucleic94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib/all_amino94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib/all_aminoct94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib/all_aminont94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib/ions94.lib
Loading library: /home1/Bis/tru/amber8-pgi-5.2-4+gcc/dat/leap/lib/solvents.lib
  Solute vdw bounding box: 6.053 5.036 4.754
  Total bounding box for atom centers: 26.053 25.036 24.754
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 28.912 28.370 27.815 angstroms.
  Volume: 22814.792 A^3
  Total mass 8402.468 amu, Density 0.612 g/cc
  Added 464 residues.
        Quit 

-- 
Dr Tru Huynh          | http://www.pasteur.fr/recherche/unites/Binfs/
mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France  
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