Re: Re: build charm++ and namd

From: Vlad Cojocaru (
Date: Thu Jul 31 2008 - 07:57:36 CDT

Hi Peter,

Well -O3 works fine for everything on the first machine I compiled. I
compiled everything with -O3 and I didn't run into problems.... the namd
executable is as fast as the one provided on the namd site of the
corresponding platform ... so I didn't see any issue with it ...

I don't know if I am right but I could guess that the problem I see has
something to do with the shell... My guess is that one of the
invocations of the cat command is not correctly processed by the shell
... And since the shell might be different on the new machine comparing
to the one I tested before .... I'll look into that ....

Of course I know that it could be that the charm people might understand
better what's happening but before I subscribe to a new list I tried to
see if one of the people routinely compiling NAMD has seen such a thing
before ... If I cannot find the solution I'll see with the charm people ...



Peter Freddolino wrote:
> Hi Vlad,
> for nontrivial charm++ issues, you're more likely to have success with
> the charm++ people (, most of whom don't read namd-l.
> BTW, is there any particular reason you're compiling with -O3? charm++
> isn't the sort of code that's likely to benefit from this, and since
> charm++ is usually compiled at -O2, it's conceivable for you to run
> into something that the higher optimization breaks (this isn't your
> problem here, but I figured I'd note it).
> Best,
> Peter
> Vlad Cojocaru wrote:
>> Just to follow up on the previous email, it seems that during build a
>> strange thing happen.
>> The 2 lines below appear in my build.log file (just before the errors
>> I posted in my previous mail):
>> cat >pup_f.f90
>> chmod a+x pup_f.f90
>> This obviously makes no sense at it cats the sh script
>> (src/util/ into the fortran file and that's why I got
>> the reported errors (the fortran compiler tries to compile an .sh
>> script). However, the build script does not contain these 2 lines so
>> I dont know where they come from ... Even more strange is that
>> yesterday I build charm++ 6.0 on another opteron machine without any
>> problem with exactly the same build I use here...
>> Vlad
>> Vlad Cojocaru wrote:
>>> Dear NAMD users,
>>> I have a problem building charm++ (version 6.0) and namd on a
>>> cluster with AMD Barcelona chips using intel 10.1.015 compiler.
>>> My build command is:
>>> ./build charm++ net-linux-amd64 icc10amd tcp --no-build-shared
>>> -DCMK_OPTIMIZE=1 -O3 2>&1 | tee build.log
>>> Although the build appeared successful (megatest passed), I got the
>>> error attached during the build.
>>> Is this something I should worry about? Has anybody seen this before ?
>>> Thanks
>>> Best wishes
>>> vlad

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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