[Pw_forum] kubuntu+gfortran+configure+make all=no executables

Paul M. Grant w2agz at pacbell.net
Wed Oct 24 21:05:37 CEST 2007

Axel, just before opening your note, I was able to run example01!  This
shows you how little I understand bash and pathing (that's what's it called
in DOS...and OS/2 Warp) in Linux.  I then went to my /home and typed in the
full path to pw.x and it ran...well, sort of...no input, of course.

Thanks, and I'll now read the rest of your note!

Paul M. Grant, PhD
Principal, W2AGZ Technologies
Visiting Scholar, Applied Physics, Stanford University
EPRI Science Fellow (Retired)
IBM Research Staff Member Emeritus
w2agz at pacbell.net

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Axel Kohlmeyer
Sent: Wednesday, October 24, 2007 11:57 AM
To: Paul M. Grant
Cc: pw_forum at pwscf.org
Subject: Re: [Pw_forum] kubuntu+gfortran+configure+make all=no executables

On Wed, 24 Oct 2007, Paul M. Grant wrote:

hi paul,

PG> First of all, thanks to Baris, Joerg and Paolo for getting back so
PG> guys are great.  

yep. they are. it is nice to see a forum, where there are
many people answering questions and not just one or two. ;-)


PG> I'm in a directory ~/espresso-3.2.3/bin console window, and when I type
PG> -lsh pw.x" I get
PG> 0 lrwxrwxrwx 1 pmpgrant pmpgrant 10 2007-10-23 23:09 pw.x -> ../PW/pw.x

ok. this is the way QE works. you have a collection of so-called
symbolic links in the bin directory pointing to the corresponding 
executables. compared to windows a symbolic link is like those
.lnk files, i.e. an entry in a directory the redirects elsewhere.
only that in the linux/unix case it is most transparent.

PG> Now there is no pw.x in PW (only holds .o and .f90 files) and I think
PG> this is saying that Linux thinks the pw.x in ~/bin is a "0-byte link" to
PG> executable "somewhere."

are you sure of that? 

PG> Yet when I open ~/bin in Dolphin (the new KDE file manager), the Details
PG> view shows that the file pw.x is 2.7 MB in size!  At the bottom of the

that means, that the symbolic link is actually pointing somewhere.
you can verify this very easily by doing: file bin/pw.x
this will tell you whether the link works or is 'broken'.

PG> window, Dophin reports (I wish screenshots could be sent to the forum)
PG> -> ../PW/pw.x Executable File (Link)"  It's as if the Linux "Link Editor
PG> (that's old IBM jargon.what's it called here? make.x?)" got confused and
PG> assigned a link attribute to what is really an executable binary file.
PG> same pattern holds true for all the QE .x files to be found in ~/bin.
PG> bet if the "l" attribute can be removed, I'll have an executable (how
can I
PG> do this.chmod?).

nope this attribute cannot be removed and it is not an artefact of the 
linker (its name is ld, btw). a symbolic link, like a directory, a fifo,
a socket or a device node is a special filesystem entry with special
semantics and those cannot be changed with chmod. if the linker fails
it usually deletes the resulting partial object, or (and this is what
might have happened) it will leave a file without executable 

PG> Thanks again, and I will get back with details on the problems
PG> Intel compiler is having with Ubuntu 7.10 which I think is a bug in the
PG> former.

it is actually about as likely, that ubuntu 7.10 is using a very new
glibc that introduces yet another quirkiness which results in 
backward incompabibility of binaries. it would not be the first time.

please note, that the intel compilers (which version are you using btw)
are only verified on a subset of linux machines, and particularly 
putting it on a new release is always risky. there may be some changes
in libraries, and/or linker that are not handled by the linker/runtime
of the intel compilers.


PG> -Paul
PG> Paul M. Grant, PhD
PG> Principal, W2AGZ Technologies
PG> Visiting Scholar, Applied Physics, Stanford University
PG> EPRI Science Fellow (Retired)
PG> IBM Research Staff Member Emeritus
PG>  <mailto:w2agz at pacbell.net> w2agz at pacbell.net
PG>  <http://www.w2agz.com/> http://www.w2agz.com

Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.
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