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.
On 3/27/07, Ross Walker <ross.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.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.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *bertrand russell
> *Sent:* Monday, March 26, 2007 22:58
> *To:* amber.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Mar 28 2007 - 06:07:43 PDT
