Hi, Nick
Thank you. Sorry, I did not notice hdf5 is in the root directory of FreeON now.
It is a bit weird, I found the wait.h in /usr/include/sys and also added -I/usr/include in FreeON/Makefile, but I still got the same error.
However, when I tries to compile Spawn.c manually by "icc -c -g -O3 -no-prec-div -fpe0 -xHost Spawn.c" (I got #define CFLAGS_STRING "-g -O3 -no-prec-div -fpe0 -xHost" in config.log), it passed ... really weird. By the way, do you know how to make the compiling
process echo the compiler flags explicitly on screen, not only:
PPFC RhoTools.o
PPFC RhoBlok.o
Then I will know what the compiler exactly did for Spawn.c. Thank you.
Cheers
Gao
From: freeon-devel-bounces+address@hidden [freeon-devel-bounces+address@hidden on behalf of Nicolas Bock address@hidden
Sent: Wednesday, May 02, 2012 11:45 PM
To: address@hidden
Subject: Re: [FreeON-devel] [Freeon-users] freeon documentation
Hi Gao,
This macro (WCOREDUMP) should be defined in <sys/wait.h>, so the fact that it's not there is a little strange. In order to narrow this down, can you build freeon with the internal lapack?
./configure FC=ifort F77=ifort CC=icc --enable-internal-lapack --enable-internal-hdf5
Thanks,
nick
On Wed, May 2, 2012 at 2:51 PM, Gao Bin
<address@hidden> wrote:
Hi, Nick
Ha, I am going to write to you :-) Sorry, I have some problems:
There is no HDF5 in Modules, but it does not matter, since HDF5 library has been installed on our computer clusters. Then I do:
./configure FC=ifort F77=ifort CC=icc LDFLAGS="-L/global/apps/intel/mkl/ 10.1.0.015/lib/em64t -lmkl -lguide -lpthread" LIBS="-Wl,-rpath,/global/apps/intel/mkl/ 10.1.0.015/lib/em64t"
--with-hdf5=/global/apps/hdf5/1.8.2/
but got the following error
make[2]: Entering directory `/home/gaobin/freeon-beta-2012-05-01/FreeON'
checking MondoLocalVersion.h
MondoLocalVersion.h unchanged
FCLD FreeON
Spawn.o: In function `spawn_':
/home/gaobin/freeon-beta-2012-05-01/FreeON/Spawn.c:200: undefined reference to `WCOREDUMP'
Spawn.o: In function `spawn':
/home/gaobin/freeon-beta-2012-05-01/FreeON/Spawn.c:243: undefined reference to `WCOREDUMP'
make[2]: *** [FreeON] Error 1
Do you know the reason? Thank you.
Cheers
Gao
Sent: Wednesday, May 02, 2012 10:34 PM
To: address@hidden
Subject: Re: [FreeON-devel] [Freeon-users] freeon documentation
Hi Gao,
did it work now?
nick
On Tue, May 1, 2012 at 3:52 PM, Gao Bin
<address@hidden> wrote:
Hi, Nick
Thank you. But the link is not valid, could you please check?
Cheers
Gao
Hi,
I uploaded a new version of the code, including the fixes Matt just mentioned, to our downloads area.
Please let us know if you run into any problems building this release.
nick
On Tue, May 1, 2012 at 11:20, Matt Challacombe
<address@hidden> wrote:
Hi GB,
This has been fixed in a beta version. We'll try to release a tar of the beta soon.
Best, Matt
On 04/30/2012 12:54 PM, Gao Bin wrote:
Hi, Matt
Thank you. It is my fault, I thought I could use FreeON without "make install". I have solved the problem. But again I have some new questions:
(1) I have tried H2.inp in Validate/SinglePoint/Restricted, it passed. But I wonder if it possible to run some commands by executing all the tests in Validate?
(2) When I tried H2O.inp in examples, I got some different error:
JForce :: RhoEcon = 2.88462, Gaussians = 78
Counting error in IntegrateNCollate
GOING DOWN GOING DOWN GOING DOWN GOING DOWN GOING DOWN
<< Counting error in IntegrateNCollate>>
GOING DOWN GOING DOWN GOING DOWN GOING DOWN GOING DOWN
Unknown error:</usr/local/bin/JForce H2O_8468 ForceEvaluation 7 1 1 7 1 1 /tmp/FreeON-scratch-H2O_8468-ugp7u9/>
I also enclosed the output file in the attachment. Could you please help me fix this error? Thank you.
Cheers
Gao
________________________________________
From: freeon-users-bounces+bin.gao=uaddress@hidden [freeon-users-bounces+bin.gao=address@hidden] on behalf of Matt Challacombe [address@hidden]
Sent: Monday, April 30, 2012 8:32 PM
To: address@hidden
Subject: Re: [Freeon-users] freeon documentation
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
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