----- Original Message -----
From: "Scott Brozell" <sbrozell.scripps.edu>
To: <amber.scripps.edu>
Sent: Wednesday, May 16, 2007 11:42 AM
Subject: Re: AMBER: AMBER8 compiler with intel 9.1 compiler
> Hi,
>
> On Tue, 15 May 2007, Peter Z. Qin wrote:
>
>> I am running AMBER8 on our school mainframe (Linux cluster). Recent
>> changes
>> at this facility forces me to re-compile AMBER8 with an Intel 9.1
>> compiler.
>> While my previous compilation of AMBER8 using an Intel 8.1 compiler
>> passed
>> all tests, the re-compilation (both the serial and the parallel version)
>> fails testing on several cases. A typical example, generated from
>> test/cytosine/Run.cytosine, is:
>>
>> 87,88c87,88
>> < NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.21
>> PRESS -5.8
>> < Etot = -608.3990 EKtot = 1063.0604 EPtot
>> -1671.459
>> ---
>> > NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.68
>> > PRESS -651.0
>> > Etot = -606.7460 EKtot = 1064.7135 EPtot
>> > -1671.459
>> 92c92
>> < EKCMT = 176.9122 VIRIAL = 180.9720 VOLUME =
>> 32637.922
>> ---
>> > EKCMT = 176.9122 VIRIAL = 635.6568 VOLUME =
>> > 32637.922
>> 94c94
>> < Ewald error estimate: 0.1512E-1
>> ---
>> > Ewald error estimate: 0.6367E+1
>>
>> My question is whether these differences are significant? and iff so,
>> whar
>> could be the fix?
>
> These are sig. diffs.
I guess that is the case, but it is still good to confirm. Thanks.
> What is the outpout of ifort -V ?
[pzq.hpc-login1 src]$ ifort -V
Intel(R) Fortran Compiler for 32-bit applications, Version 9.1 Build
20060323Z Package ID: l_fc_p_9.1.032
Copyright (C) 1985-2006 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY
> What config file was used ?
[pzq.hpc-login1 src]$ more config.h
#==============================================================================
# AMBER Makefile configuration for compiler/architecture: ifort
# Generated via command: ./configure ifort
#
# Configuration script written mainly by Joe Krahn, Scott Brozell, and
# Dave Case, with contributions from lots of people.
#==============================================================================
#------------------------------------------------------------------------------
# Main AMBER source root directory
#------------------------------------------------------------------------------
AMBER_SRC=/home/rcf-12/pzq/MD/amber8/src
#------------------------------------------------------------------------------
# AMBERBUILDFLAGS provides a hook into the build process for installers;
# for example, to build debug versions of the amber programs
# make -e AMBERBUILDFLAGS="-DDEBUG -g"
#------------------------------------------------------------------------------
AMBERBUILDFLAGS=
#------------------------------------------------------------------------------
# LOCALFLAGS is intended for program specific modifications to the
# Fortran build process and may be modified by the program's local makefile
#------------------------------------------------------------------------------
LOCALFLAGS=
#------------------------------------------------------------------------------
# Availability and method of delivery of math and optional libraries
#------------------------------------------------------------------------------
USE_BLASLIB=$(SOURCE_COMPILED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)
#------------------------------------------------------------------------------
# C compiler
#------------------------------------------------------------------------------
CC= gcc
CPLUSPLUS=g++
ALTCC=gcc
CFLAGS=-O2 $(AMBERBUILDFLAGS)
ALTCFLAGS= $(AMBERBUILDFLAGS)
CPPFLAGS= $(AMBERBUILDFLAGS)
#------------------------------------------------------------------------------
# Fortran preprocessing and compiler.
# FPPFLAGS holds the main Fortran options, such as whether MPI is used.
#------------------------------------------------------------------------------
FPPFLAGS= -P -I$(AMBER_SRC)/include $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= ifort
FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -w95 -mp1 -ip -O3 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FPP_PREFIX= _
FREEFORMAT_FLAG= -FR
#------------------------------------------------------------------------------
# Loader:
#------------------------------------------------------------------------------
LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB=
LOADPTRAJ= ifort -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
#------------------------------------------------------------------------------
# Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES: .f90
SYSDIR=lib
AR=ar rv
M4=m4
RANLIB=ranlib
SFX=
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
# default rules for Fortran and C compilation:
.f.o: $<
$(FPP) $< > $(FPP_PREFIX)$<
$(FC) -c $(FFLAGS) -o $. $(FPP_PREFIX)$<
.f90.o: $<
$(FPP) $< > $(FPP_PREFIX)$<
$(FC) -c $(FFLAGS) -o $. $(FPP_PREFIX)$<
.c.o:
$(CC) -c $(CFLAGS) $(CPPFLAGS) -o $. $<
> What are the machine details ?
hpc0001 hpc0256 256 Dual Dualcore AMD Opteron 2.0 GHz
4GB Memory 60GB main large quick X4100 opteron x86_64 dualcore
more details at
http://www.usc.edu/hpcc/systems/use-l-0
>
> The simplest fix is to use an older intel compiler.
I was told by the adminstrator that intel 8.1 is no longer support on the
operating system
> I stay away from the latest from intel because I have found their
> quality assurance to be lacking.
> On the machines I use the latest versions are
> ia32 intel-compilers-9.0-20050916
> ia64 intel-compilers-9.1-20070111
> but I have not built amber with these versions (using 8.1 instead).
> I could not quickly find details about which intel versions
> have been used to build Amber at the web site.
> Other posters may be helpful here.
>
> The likely cause is changes in code meaning due to compiler
> optimizations. If you cannot use an older ifort then one
> could reduce the optimization level. There are clues in the diffs
> above, and more info about the other failing tests might enable
> someone knowledgeable about Amber's software architecture
> to identify a small number of files that have been affected.
>
1. For the cytosine case, below is the full difference between the
cytosine.out.save (from 02/2004) and my cytosine.out. It seems the input
parameters for sander are different, which is consistent with compiler
optimization level. But how do I reduce the optimization?
[pzq.hpc-login1 cytosine]$ more full.dif.cytosine
6c6
< | Run on 02/05/2004 at 17:33:30
---
> | Run on 05/15/2007 at 17:29:37
44c44
< | Flags: MPI
---
> | Flags:
60c60
< | Real 170832
---
> | Real 166979
62,64c62,64
< | Integer 100948
< | Max Pairs 26479
< | Max Rstack 43100
---
> | Integer 155255
> | Max Pairs 423666
> | Max Rstack 117560
66c66
< | Total 2224 kbytes
---
> | Total 4539 kbytes
131,136d130
< | Atom division among processors:
< | 0 81 161 241 321 401 481 561
< | 641 721 801 881 961 1041 1121 1196
< | 1271
< | Running AMBER/MPI version on 16 nodes
<
152c146
< | Local SIZE OF NONBOND LIST = 6576
---
> | Local SIZE OF NONBOND LIST = 100304
155,156c149,150
< NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.21 PRESS
-5.8
< Etot = -608.3990 EKtot = 1063.0604 EPtot
= -1671.4594
---
> NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.68 PRESS
> -651.0
> Etot = -606.7460 EKtot = 1064.7135 EPtot
> = -1671.4594
160c154
< EKCMT = 176.9122 VIRIAL = 180.9720 VOLUME =
32637.9223
---
> EKCMT = 176.9122 VIRIAL = 635.6568 VOLUME =
> 32637.9223
162c156
< Ewald error estimate: 0.1512E-01
---
> Ewald error estimate: 0.6367E+01
....
2. The following tests failed in the intel 9.1 compilation but passed for
the intel 8.1 compilation. Could this give us a clue
cytosine, dhfr, dhfr.noshake,mtrx, trx.cpln, alp.
-peter
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Received on Sun May 20 2007 - 06:07:12 PDT
