AMBER Archive (2007)

Subject: Re: AMBER: Error - must define AMBERHOME environment variable

From: bertrand russell (betrussell23_at_gmail.com)
Date: Tue Mar 27 2007 - 12:42:57 CST

On 3/28/07, bertrand russell <betrussell23_at_gmail.com> wrote:
>
> Dear Mr.Ross,
>
> As you suggested I downloaded the latest bugfix.allfile available from
> amber.scripps.edu site and patched it. I gave the command as you specified
> in your mail.
>
> >./configure -nopar sgi_altix
> >make serial
> I am getting the following error which I was not getting before ( when I
> used only 32 bugfixes my compilation went fine at this stage ). Could you
> point what I am doing wrong? Thanks in advance.

##############################################################################

bash-2.05b$ make serial
Starting installation of Amber9 (serial) at Tue Mar 27 23:48:15 IST 2007.
cd lib; make install
make[1]: Entering directory `/pludisk1/oth/amber/amber9/src/lib'
cpp -traditional -P new2oldparm.f > _new2oldparm.f
ifort -c -w95 -ftz -O2 -o new2oldparm.o _new2oldparm.f
cpp -traditional -P nxtsec.f > _nxtsec.f
ifort -c -w95 -ftz -O2 -o nxtsec.o _nxtsec.f
ifort -i-static -o new2oldparm new2oldparm.o nxtsec.o
/usr/bin/ld: --relax and -r may not be used together
make[1]: *** [new2oldparm] Error 1
make[1]: Leaving directory `/pludisk1/oth/amber/amber9/src/lib'
make: *** [serial] Error 2

##############################################################################

On 3/27/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:
> >
> > Dear Bertrand,
> > Firstly on an sgi_altix you should use:
> >
> > ./configure -nopar sgi_altix (for the non-parallel version, best to
> > get this working first)
> >
> > and
> >
> > ./configure -mpi sgi_altix (for the parallel version.)
> >
> > this way the correct libraries and compiler flags should be set.
> >
> > The segfault is coming from the compiler and is a bug in the compiler
> > itself and there is not a lot we can do about it other than try to work
> > around it. This is Intel's fault and they should fix it. The problem is made
> > more complicated by the fact that some versions of the compiler work fine
> > while others crash. And even worse when you go to a newer compiler some
> > previous bugs are fixed and yet newer ones are introduced :-(.
> >
> > Firstly though, what version of the compiler are you using? You should
> > go and get the very latest compiler just in case some of the bugs may have
> > been fixed.
> >
> > Next obtain bugfix.all from the bugfixes page on amber.scripps.edu and
> > patch your source code with it.
> >
> > Then cd $AMBERHOME/src
> >
> > make clean
> > make
> >
> > See how far the compiler gets before it segfaults. The following only
> > applies to the compilation of files in $AMBERHOME/src/sander. If the
> > compiler dies on a file outside this directory then please send me the make
> > log. If it segfaults on a specific file in src/sander then
> >
> > cd $AMBERHOME/src/sander
> >
> > edit that file and remove the first line of the file that reads "!
> > <compile=optimized>"
> >
> > Next do "rm -f depend"
> > makedepend > depend
> > cd ..
> > make
> >
> > Hopefully it will proceed beyond that file and perhaps segfault
> > somewhere else or maybe compile successfully. If it still segfaults on the
> > same file then edit $AMBERHOME/src/config.h and change
> >
> > FFLAGS= -w95 -ftz -O2 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> > to
> > FFLAGS= -w95 -ftz -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> >
> > Then try make again.
> >
> > Hopefully this will allow you to build a working copy of sander. Next
> > run the test cases and see how it does. Let me know if it fails on any,
> > particularly the QMMM ones since some versions of the Intel compilers had
> > problems with qm_link_atoms.f then let me know and I can explain how to work
> > around this compiler bug as well.
> >
> > Failing all of the above see if you can get hold of ifort v8.1.025 for
> > Itanium (IA64) since this version I know to work out of the box.
> >
> > Good luck....
> >
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not be read every day, and should not be used for urgent or sensitive
> > issues.
> >
> >
> > ------------------------------
> > *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > Behalf Of *bertrand russell
> > *Sent:* Monday, March 26, 2007 22:58
> > *To:* amber_at_scripps.edu
> > *Subject:* Re: AMBER: Error - must define AMBERHOME environment variable
> >
> > Dear Mr.Ross,
> >
> > Thank you for your support. I herewith sending you
> > the compiler error message which I got while compiling with ifort_ia64
> > compiler. The steps I followed are and the error message is as follows,
> >
> > >cd $AMBERHOME/src
> > >./configure -p4 ifort_ia64
> > After this point I edited the the config.h file by adding "-ldl" flag
> > immediately following ifort wherever it is in the config.h file. Then I
> > issued the following command,
> > >make serial
> > My error messages are as follows,
> >
> > ##########################################################
> > ifort -ldl -c -w95 -ftz -O2 -FR -o mdread.o _mdread.f
> > cpp -traditional -P rdparm.f > _rdparm.f
> > ifort -ldl -c -w95 -ftz -O2 -FR -o rdparm.o _rdparm.f
> > cpp -traditional -P getcor.f > _getcor.f
> > ifort -ldl -c -w95 -ftz -O2 -FR -o getcor.o _getcor.f
> > cpp -traditional -P sa_driver.f > _sa_driver.f
> > ifort -ldl -c -w95 -ftz -O3 -IPF_fma -IPF_fp_relaxed -ip -FR -o
> > sa_driver.o _sa_driver.f
> > cpp -traditional -P pb_force.f > _pb_force.f
> > ifort -ldl -c -w95 -ftz -O3 -IPF_fma -IPF_fp_relaxed -ip -FR -o
> > pb_force.o _pb_force.f
> > fortcom: Severe: _pb_force.f, line 1597: **Internal compiler error:
> > segmentation violation signal raised** Please report this error along with
> > the circumstances in which it occurred in a Software Problem Report. Note:
> > File and line given may not be explicit cause of this error.
> > end function ey
> > ^
> > compilation aborted for _pb_force.f (code 3)
> > make[1]: *** [pb_force.o] Error 3
> > make[1]: Leaving directory `/pludisk1/oth/amber/amber9/src/pbsa'
> > make: *** [serial] Error 2
> > bash-2.05b$
> > ########################################################
> >
> > If I reduce the optimisation level to "O2" instead of "O3" I am getting
> > the same error but at 1616 line number instaead of 1597th line. It would be
> > helpful if I can solve this problem and install amber9 in our SGI Altix. I
> > patched with the latest bugfix.all file from amber.scripps.edu site.
> >
> > My machine specifications:
> > Machine Name: Altix 390
> > Processor Type: Intel Itanium
> > Operating system: ALTIX SGI Propack
> > ifort compiler version: Version 8.0
> >
> > Many thanks in advance.
> >
> >
>
>
> --
> Live Life; Don't pass it
> Bertrand.P.S.Russell
> +91-9894398441
> 

-- 
Live Life; Don't pass it
Bertrand.P.S.Russell
+91-9894398441

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