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Re: [Freeon-users] freeon documentation


From: Gao Bin
Subject: Re: [Freeon-users] freeon documentation
Date: Mon, 30 Apr 2012 16:58:44 +0000

Hi, Nick

Thank you for your help. I have solved the problem:

(1) The reason I could not configure hdf5-1.8.3 is it requires libtool with version at least 2.2 (line 976 in hdf5-1.8.3/configure.in). I do not know the version of my libtool, I just simply commented this requirement from HDF5. It works :-), but I have encountered some problems when compiling QCTC/Density.f90, which requires Globals module. I thought compiler or automake tools should figure out the dependence of these modules, but they did not on my MacBook. So I manually changed the order of Globals.f90 and Density.f90 in QCTC/Makefile.am. Then I got the executable FreeON.

(2) I have also tried freeon-2011-11-03.tar.bz2. It can also be compiled but there is only SinglePoint in Validate, I have to manually remove other entries in configure and Validate/Makefile. Is it a bug in this release?

Anyway, I have got FreeON executable in both case, but I am sorry that I have some further problems:

(1) When I compiled FreeON from the repository instead of freeon-2011-11-03.tar.bz2, I have got the problem about making "localversion". Since I did not know what it is, I just simply commented it in Makefile.am. But I am not sure what I did is correct or not?

(2) In both cases, I have got the problem when I tried to run a simple example H2O.inp in "examples" directory. I have set up some variables in my $HOME/.bash_profile as:

export PATH=$PATH:/Users/gaobin/Work/XKjem/freeon/FreeON
export MONDO_HOME=/Users/gaobin/Work/XKjem/freeon
export MONDO_EXEC=/Users/gaobin/Work/XKjem/freeon/FreeON/FreeON #I am not sure if this is correct?
export MONDO_SCRATCH=/tmp

Then I ran "FreeON H2O.inp", and it printed something on screen:

FreeON : LoadCommand             :: env variable $(MONDO_HOME) set to /Users/gaobin/Work/XKjem/freeon
FreeON : LoadCommand             :: env variable $(MONDO_EXEC) set to /Users/gaobin/Work/XKjem/freeon/FreeON/FreeON
FreeON : LoadCommand             :: env variable $(MONDO_SCRATCH) set to /tmp
FreeON : LoadCommand             :: input file H2O.inp
FreeON : LoadCommand             :: SCF name H2O_73662
... ...
SCF                              :: doing SCF
Invoke                           :: invoking MakePFFT
Invoke : Clump 1                 :: /Users/gaobin/Work/XKjem/freeon/FreeON/FreeON/MakePFFT H2O_73662 OneElectronMatrices 0 1 1 0 1 1 /tmp/FreeON-scratch-H2O_73662-6DXNki/
error with execvp: Not a directory
Invoke : errorcode = -674034     :: </Users/gaobin/Work/XKjem/freeon/FreeON/FreeON/MakePFFT H2O_73662 OneElectronMatrices 0 1 1 0 1 1 /tmp/FreeON-scratch-H2O_73662-6DXNki/>
Invoke : Clump 1                 :: MakePFFT H2O_73662 OneElectronMatrices 0 1 1 0 1 1 /tmp/FreeON-scratch-H2O_73662-6DXNki/
error with execvp: No such file or directory
Invoke : errorcode = -674034     :: <MakePFFT H2O_73662 OneElectronMatrices 0 1 1 0 1 1 /tmp/FreeON-scratch-H2O_73662-6DXNki/>
Invoke                           :: failed to spawn process
This is fatal
 GOING DOWN GOING DOWN GOING DOWN GOING DOWN GOING DOWN
 <<This is fatal>>
 GOING DOWN GOING DOWN GOING DOWN GOING DOWN GOING DOWN
Abort trap

I noticed the error is due to some checks in FreeON/Spawn.c (error with execvp), but I do not how to solve it. I have also enclosed the output file in the attachment. Could anyone please help me?

Thank you in advance.

Cheers

Gao


From: Nicolas Bock address@hidden
Sent: Friday, April 27, 2012 7:30 PM
To: Gao Bin
Cc: address@hidden
Subject: Re: [Freeon-users] freeon documentation

Hi Gao,

we don't have a Mac to try this out, so I am going to have to guess a little bit. I noticed that you are using gcc from XCode tools which is pretty old (4.0.1) and a much more recent Fortran frontend (4.4.0). Try to use the newer gcc for C also, i.e. you should pass

CC=/usr/local/bin/gcc

to configure as well.

You clone from git and rebuild the configure scripts using your local versions of autoconf/automake/libtool and the error you are seeing might have to do with differences in autoconf/automake/libtool versions between your laptop and our machines. Could you try to download a tar file from


which already includes a prebuilt configure script? Once unpacked you can run configure right away and don't have to autoreconf.

Thanks,

nick



On Fri, Apr 27, 2012 at 02:04, Gao Bin <address@hidden> wrote:
Hi, Nick

Please kindly check the config.log of hdf5-1.8.3 in the enclosed file. Thank you.

I cloned a version of FreeON from http://git.savannah.gnu.org/cgit/freeon.git (using git clone git://git.sv.gnu.org/freeon.git). I think it might be the latest one with "commit aeed6ff6c93d16d05cb78c10331eec9675dda524".

Cheers

Gao

From: Nicolas Bock [address@hidden]
Sent: Friday, April 27, 2012 5:26 AM
To: Gao Bin
Cc: address@hidden

Subject: Re: [Freeon-users] freeon documentation

Hi Gao,

the configure process died while configuring hdf5. Could you send me Modules/hdf5-1.8.3/config.log? What version of FreeON are you trying to build? Did you download it as a tar file?

nick


On Thu, Apr 26, 2012 at 16:04, Gao Bin <address@hidden> wrote:
Hi, guys

I am trying to compile FreeON on MacBook today, using gfortran (GNU Fortran (GCC) 4.4.0 20090123 (experimental) [trunk revision 143587]). What I did is:

./reconfigure.sh
./configure

but I got the following error message:

checking if srcdir= and time commands work together... yes
./configure: line 22618: syntax error near unexpected token `2.2'
./configure: line 22618: `LT_PREREQ(2.2)'
configure: error: ./configure failed for Modules/hdf5-1.8.3

The line 22618 in configure is:

eval "echo \"\$as_me:$LINENO: $ac_try_echo\"") >&5

However, I can not figure out the problem based on this information. Could you please help me?

P.S. I also send the config.log in the enclosed file, hope it helps. Thank you in advance.

Cheers

Gao

From: Nicolas Bock [address@hidden]
Sent: Friday, April 20, 2012 6:48 PM
To: address@hidden; Gao Bin

Subject: Re: [Freeon-users] freeon documentation

Hi Gao,

we don't have a good manual or more in depth documentation at the moment, but are working on it. In the meantime you may want to have a look at the examples and Validate directories.

MPI is currently only working for NEB calculations, and that only across the band, i.e. each clone will be run on a separate rank.

If you have some specific input file questions, just email us back here and we will walk you through the input file syntax and the options you need to set.

nick


On Fri, Apr 20, 2012 at 05:57, Gao Bin <address@hidden> wrote:
Hi,

I heard MondoSCF long time ago, and would like to use it. Once I knew FreeON the early of this week, I have cloned a copy. Although it seems to be easy to use from the examples, yet may I ask if there is any FreeON documentations or tutorials?

Moreover, it looks like that FreeON can work with MPI (by searching "call mpi" in the source code), is it right?

Thank you in advance!

Cheers

Gao



Attachment: H2O_73662.out
Description: H2O_73662.out


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