Re: Re: segmentation fault when running ABF

From: Vlad Cojocaru (
Date: Wed Aug 06 2008 - 11:23:45 CDT

Hi Alex.

Thanks a lot for the advices.. I was just writing the lines below when I
got your email. The reason I tried with "-static" before was because
that's what it appears in the default Linux-amd64-icc.arch file .....

 I succeeded to compile the cvs code of namd correctly (with the
specifications mentioned in the emails below) and namd is able to run
tclforces scripts (including abf) if linked to my own compilation of
tcl8.4.19 with -DUSE_NON_CONST in CFLAGS.

Also, the provided (on the namd website) precompiled tcl libs work as
long as the "-static" option of icc is not used.

Best wishes

Axel Kohlmeyer wrote:
> On Wed, 6 Aug 2008, Vlad Cojocaru wrote:
> VC> Hi Alex,
> hi vald!
> VC> Well .. I tried to compile using my own compilation of tcl8.5 because when
> VC> trying with the precompiled libs (for linux-amd64) from the namd webpage
> VC> (with the -static option added to the icc compiler) I get the error1 (see
> why add -static??? linking completely statically is a "bad idea(tm)"
> on any machine using glibc-2. furthermore, there is no gain from
> using intel compiler to compile TCL. you are much better off using
> gcc/g++ for everything that is not time critical as that will reduce
> the dependencies on runtime libraries. particularly in libraries
> that can be pretty nasty. on linux machines, you always have to depend
> on the gcc runtime (why that one has to be dynamical i cannot
> comprehend, but this is not the forum to discuss it).
> VC> below). Second, when I tried to compile tcl 8.3.5 I get a configure error
> use gcc to compile and drop the -static and it will work.
> moreover, if your distribution provides a prepackaged tcl,
> why go through the pains of building your own?
> VC> (error2 below). When I looked for the configure error on the tcl webpage I
> VC> found the answer "tcl8.3.5" is an old verison .. if you upgrade, tcl should
> VC> configure correctly". Then I thought OK .. I use the latest tcl and I should
> VC> be fine .... So, that's the background of it ..
> yep. there is just one thing that one has to consider. using the
> latest/greatest is usually OK with simple (small) applications as
> those can be adapted quickly and with rather little effort, if needed.
> but large complicated packages (like NAMD, VMD and many others) are
> a different beast: first of all you want the application to excecute
> absolutely correctly, always, then it has to be portable to many
> platforms, many of which are "old", some even "legacy" and finally,
> there are a frighteningly small number of people actually working on
> maintaining and updating those codes. as a consequence progress is
> usually very slow (you don't want to break anything that was working
> and have to validate everything that gets added). it is especially scary
> if one considers how many people actually put their trust into those
> application and it is sometimes depressing to see how little respect
> is being paid for all the hard work (and i mean respect as in actually
> contributing to the effort, which is the best way to make sure that
> free applications like NAMD do see more development in the future).
> VC> I also tried to add -DUSE_NON_CONST to my tcl8.5 compilation but still in
> VC> vain ....
> VC>
> VC> Now, I guess I should try tcl 8.4 ..... as it seems that nobody has tried to
> VC> build namd with tcl8.5 ...
> VC> For the record, I am trying on two different machines, both amd64
> VC> architectures, on both intel 10.1.015 compilers. the namd code was
> VC> downloaded from the cvs a week ago ...
> i would actually try building with gcc/g++ first.
> most of the time you have a better chance to get a
> working executable and _then_ you can try to see if
> you get a better/faster binary from intel.
> the most important lesson in building package software
> is to do it in stages, starting defensively and then
> gradually move in stages to the full featured option
> with all bells and whistles and optimizations.
> cheers,
> axel.
> VC> Best wishes
> VC> vlad
> VC>
> VC> ---------------------------------------error2----------------------------------------------------------------------------------------------
> VC> checking system version (for dynamic loading)... ./configure: line 6208:
> VC> syntax error near unexpected token `)'
> VC> ./configure: line 6208: ` OSF*)'
> VC>

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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