Hi Oliver,

Sorry for the inconvenience ...  Reading/writing in gz format is still developmental in APBS, we didn't test them over all platform/compiler combination. As for Linux, I tested your examples on a 32-bit CentOS box with the latest Intel compilers (icc/ifort 12.0.0), and it worked just fine, I got the same results as on Mac OS X.



On Mon, Dec 13, 2010 at 9:15 AM, Oliver Beckstein <oliver.beckstein@bioch.ox.ac.uk> wrote:
Hi Yong,

A while back you fixed the issue of reading dx.gz files in svn1623.

I reported this as fixed:

On 22 Nov, 2010, at 18:50, Oliver Beckstein wrote:

> svn1623 is working as it is supposed to – my test case (with your fixes...) gives exactly the same total energy.

However, that was a bit premature.

* When I compile with gcc/gfortran on Mac OS X/Darwin then it seems to be working; the attached test case gives the same total energy, regardless of using gzipped or plain dx files.

* When I compile on Linux Ubuntu 8.04/9.04/10.04 on either i686 (32 bit) or x86_64 (64 bit) I will either get different answers (with the plain dx total energy being the same as on Darwin---on x86_64) or even fail to solve (on i686) as shown here:

Parsing input file solv_dxgz.in...
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from 1OED.pqr.
% BUILDBAND: dpbfa problem:  1
% BUILDBAND: leading principle minor not PD...
% BUILDOPS: changing your MGSOLV
% BUILDOPS: to iterative...
% MVCS: rhs is zero on finest level
% MVCS: iters on coarse grid:  100
% MVCS: iters on coarse grid:  100

(This was compiled on Ubuntu 9.04 with GNU compilers 4.3.3 and

       ./configure --prefix=$HOME/Library/
       make install


Note that the failure is ONLY observed when trying to read dx.gz files.

* I tried both gcc 4.3/4.4 and icc/ifort 9.1 or 10.1 on Linux.

* I used gcc-mp-4.4 (release 4.4.5) and gfortran-mp-4.4 from MacPorts on Mac OS X 10.6.4 or gcc/gfortran 4.4.1 on Mac OS X 10.5.8.

In order to run the tests:

       tar -jxvf TESTING.tar.bz2
       cd TESTING
       export APBS=/path/to/apbs  # if apbs is not on PATH

If everything works then you should not see a difference in 'Global net ELEC energy'. See examples below:

Example of a successful run (on Darwin):

@@ -132,5 +132,5 @@

-print energy 1 (ref0) end
+print energy 1 (ref1) end
  Local net energy (PE 0) = 7.465005631049E+02 kJ/mol
  Global net ELEC energy = 7.465005631049E+02 kJ/mol

Example of failure (GNU 4.4 on x86_64):


-print energy 1 (ref0) end
-  Local net energy (PE 0) = 7.465005631049E+02 kJ/mol
-  Global net ELEC energy = 7.465005631049E+02 kJ/mol
+print energy 1 (ref1) end
+  Local net energy (PE 0) = 1.587888288299E+03 kJ/mol
+  Global net ELEC energy = 1.587888288299E+03 kJ/mol

Sorry for the long email but I hope that this will give you enough information to get an idea of what's going on. Please let me know if you need more information.


Oliver Beckstein
SBCB Unit, University of Oxford
email: oliver.beckstein@bioch.ox.ac.uk
web: http://sbcb.bioch.ox.ac.uk/oliver/

Lotusphere 2011
Register now for Lotusphere 2011 and learn how
to connect the dots, take your collaborative environment
to the next level, and enter the era of Social Business.
apbs-users mailing list