Re: [Freeon-users] freeon documentation

[Matt Challacombe]

Does /Users/gaobin/Work/XKjem/freeon/FreeON/FreeON/MakePFFT  exist?

Can you run the invoke like, ie:
/Users/gaobin/Work/XKjem/freeon/FreeON/FreeON/MakePFFT H2O_73662
OneElectronMatrices 0 1 1 0 1 1 /tmp/FreeON-scratch-H2O_73662-6DXNki/
by itself?  See, thats the "backend" being excvp'd.  You should be
able to run each "subprogram" in the backend as a stand alone.

-M


On Mon, Apr 30, 2012 at 10:58 AM, Gao Bin <address@hidden> wrote:
> Hi, Nick/Users/gaobin/Work/XKjem/freeon/FreeON/FreeON/MakePFFT H2O_73662 
> OneElectronMatrices 0 1 1 0 1 1 /tmp/FreeON-scratch-H2O_73662-6DXNki/
>
> 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
>
> http://download.savannah.gnu.org/releases/freeon/freeon-2011-11-03.tar.bz2
>
> 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
>>>
>>>
>>
>