Hi Mikheil,
Sorry I didn't notice your previous email. From the ../configure result in your previous email:
>checking for mpirun... /usr/bin/mpirun
> configure-ac: error: LAM/MPI not working
There is an MPI inside your default path /usr. The problem is if you do not install MPI in a default path, (i.e. your last LAM installation: --prefix=/usr/local/lam), the ../configure ESPResSo will call the mpirun in /usr/bin/mpirun first and use it in the whole setting. You can install MPI with --prefix=/usr, which will replace the old MPI, but I do not suggest it because it is risky and you cannot do this if later you install in a public cluster
which you do not have a root access. What I suggest is trying to declare your environment path in your .bashrc or .bash_profile file in your home directory. If you never do this, you can googling first. The point is making the ../configure ESPResSo call the mpirun and mpi library and mpi header in your MPI installation directory first.
I prefer OpenMPI because I heard there is no serious development in LAM now. Manually installing gcc also requires much time, mostly when you get problem with its dependency. If you install with openMPI, try this in the flag:
../configure-ac CC=mpicc MPICC=MPICC --with-mpi=openmpi CPPFLAGS=... etc...
FMIIW, Good Luck,
Aang
----------------------------------------------------------------------
Message: 1
Date: Mon, 9 Aug 2010 16:29:51 -0400
From: Mikheil Azatov <
address@hidden>
Subject: Re:
[ESPResSo] parallel computing
To:
address@hiddenMessage-ID:
<
address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Hi Aang, sorry to bother you again. I think I figured out what is the
problem after a long day. So when I install lam it gives me an error that
"LAM requires a C++ compiler with support for the bool data type." I don't
know if you ever had this problem but after looking through lam forums the
only suggestion i found was to downgrade gcc version. before doing that i
thought it might be better to try other mpi's. As i understand other two
options are Open
mpi and MPICH. MPICH is not recommended in Espresso manual
(as working slower) and Open MPI is not described there at all( so i don't
know what option would I even use in ./configure --with-mpi=???) . So I was
wandering what would you suggest to do in my situation. Which one of these
to try to install or maybe keep trying with lam?
Thank you so much!!! Your help will be really appreciated!
Mikheil Azatov
University of Maryland
On Mon, Aug 9, 2010 at 11:55 AM, Mikheil Azatov <
address@hidden> wrote:
> Hi,
>
> Thanks for your help again! I tried installing espresso the way you
> suggested but I still get an error when i run the configure (as you said
> below). the error says that it didn't find lam.h. but as i look through the
> folders where lam was installed the header file is called mpi.h. I
attached
> two config.log to this e-mail. One from the espresso directory and another
> from espressso/obj-Core-pc-linux directory.
>
> Here is what I get in terminal:
> address@hidden:~/mpiespresso$ ./configure-ac --with-mpi=lam
> CPPFLAGS="-I/usr/local/lam/include/ -I/usr/include/tcl8.5"
> LDFLAGS="-L/usr/local/lam/lib" LD_LIBRARY_PATH="/usr/local/lam/lib"
> checking build system type... Core-pc-linux
> checking host system type... Core-pc-linux
> checking target system type... Core-pc-linux
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
>
****************************************************************
> * Check the compiler and MPI *
> ****************************************************************
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking for gcc option to accept ISO C89... none needed
> checking dependency style of gcc... gcc3
> checking how to run the C preprocessor... gcc -E
> checking for gcc... (cached) gcc
> checking whether we are using
the GNU C compiler... (cached) yes
> checking for gcc option to accept ISO C89... (cached) none needed
> checking dependency style of gcc... (cached) gcc3
> checking whether gcc and cc understand -c and -o together... yes
> checking for mpcc... no
> checking for mpxlc... no
> checking for mpicc... no
> checking for mpicci... no
> checking for mpiccg... no
> checking for hcc... no
> checking for cc... cc
> checking whether the cc command works out of the box for MPI... no
> configure-ac: trying to find a LAM environment
> checking whether the cc command works without additional flags... no
> configure-ac: did not find lam.h, if you want to use LAM, please specify
> its location via CPPFLAGS
> checking for mpirun... /usr/bin/mpirun
> configure-ac: error: LAM/MPI not working
> address@hidden:~/mpiespresso$ whereis lam.h
> lam: /etc/lam
/usr/lib/lam /usr/lib64/lam /usr/local/lam
> address@hidden:~/mpiespresso$ ./configure-ac --with-mpi=lam
> CPPFLAGS="-I/usr/local/lam/include/ -I/usr/include/tcl8.5"
> LDFLAGS="-L/usr/local/lam/lib" LD_LIBRARY_PATH="/usr/local/lam/lib"
> checking build system type... Core-pc-linux
> checking host system type... Core-pc-linux
> checking target system type... Core-pc-linux
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... no
> checking for mawk... mawk
> checking whether make sets $(MAKE)... yes
> checking whether to enable maintainer-specific portions of Makefiles... no
> ****************************************************************
> * Check the compiler and
MPI *
> ****************************************************************
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking for gcc option to accept ISO C89... none needed
> checking dependency style of gcc... gcc3
> checking how to run the C preprocessor... gcc -E
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking for gcc option to accept ISO C89... (cached) none needed
> checking dependency style of gcc...
(cached) gcc3
> checking whether gcc and cc understand -c and -o together... yes
> checking for mpcc... no
> checking for mpxlc... no
> checking for mpicc... no
> checking for mpicci... no
> checking for mpiccg... no
> checking for hcc... no
> checking for cc... cc
> checking whether the cc command works out of the box for MPI... no
> configure-ac: trying to find a LAM environment
> checking whether the cc command works without additional flags... no
> configure-ac: did not find lam.h, if you want to use LAM, please specify
> its location via CPPFLAGS
> checking for mpirun... /usr/bin/mpirun
> configure-ac: error: LAM/MPI not working
>
>
> Thanks again,
> Mikheil
> University of Maryland
>
>
> 2010/8/8 Ahmad A. J. Agung <
address@hidden>
>
> Hi Mikheil,
>>
>> I see your LAM installation is in /usr/local/lam folder. Try to install
>> ESPResSo with this:
>>
>> ../configure-ac --with-mpi=lam CPPFLAGS="-I/usr/local/lam/include/ -I(your
>> TCL include-folder)" LDFLAGS= "-L/usr/local/lam/lib -L(your TCL lib-folder)"
>> LD_LIBRARY_PATH="/usr/local/lam/lib:(your TCL lib-folder)"
>>
>> Set the (your TCL include-folder) and (your TCL lib-folder) according to
>> where your TCL is installed, with the form analogous to how the lam folder
>> was declared in each flag. You can make a trial with OpenMPI also, but it is
>> safer to install one MPI program at a time.
>>
>> FMIIW, Good Luck,
>> Aang.
>>
>>
----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sat, 7 Aug 2010 16:44:10 -0400
>> From: Mikheil Azatov <
address@hidden>
>> Subject: Re: [ESPResSo] ESPResSo Digest, Vol 39, Issue 2
>> To:
address@hidden>> Message-ID:
>> <AANLkTinbSOG5Lt=
address@hidden>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> Thanks Aang and Olaf,
>>
>> I uninstalled openmpi and reinstalled lam 7.1.4. I still have the problem
>> and
it looks like you were right Aang. The error looks like this:
>>
>> ....
>> ../ghosts.h:76:17: error: mpi.h: No such file or directory
>> In file included from ../cells.h:54,
>> from ../thermostat.h:24,
>> from ../energy.h:17,
>> from ../initialize.c:24:
>> ../ghosts.h:138: error: expected specifier-qualifier-list before
>> ?MPI_Comm?
>> In file included from ../pressure.h:90,
>> from ../thermostat.h:25,
>> from ../energy.h:17,
>> from ../initialize.c:24:
>> ...
>>
>> I attached
config.log's of both Espresso(from the obj-Core-pc-linux
>> directory) and Lam installation. I was not sure which of the config.log's
>> from the lam directory to send because there were a lot of them in
>> different
>> folders. So I sent you the one that was in the top directory( i.e.
>> directly
>> in lam ). Let me know if I sent the right things :)
>>
>>
>> Hope you can figure out the error,
>> It's my first week reading about parallel computing so I'm very new to
>> this
>> :)
>> Thanks,
>> Mikheil
>> University of Maryland
>>
>>
>>
>> On Sat, Aug 7, 2010 at 12:45 AM, Ahmad A. J. Agung <
address@hidden>> >wrote:
>>
>> > Hi,
>> >
>> > I
might be wrong, but in my experience, it could happen if your MPI
>> library
>> > (ie. LAM or OpenMPI library) is not in your environment path. If you
>> still
>> > face the same problem, you may send me the config.log of your MPI and
>> > Espresso installation. I will try to help.
>> >
>> > Regards,
>> > Aang
>> >
>> > ------------------------------
>> > *From:* "
address@hidden" <
>> >
address@hidden>
>> > *To:*
address@hidden>> > *Sent:* Thu, August 5, 2010 6:02:02 PM
>> > *Subject:* ESPResSo Digest, Vol 39, Issue 2
>> >
>> > Send ESPResSo mailing list submissions to
>> >
address@hidden>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> >
https://fias.uni-frankfurt.de/mailman/listinfo/espresso>> > or, via email, send a message with subject or body 'help' to
>> >
address@hidden>> >
>> > You can reach the person managing the list at
>> >
address@hidden>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of ESPResSo digest..."
>> >
>> >
>> > Today's Topics:
>> >
>> > 1. parallel computing (Mikheil Azatov)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Wed, 4 Aug 2010 11:16:29 -0400
>> > From: Mikheil Azatov <
address@hidden>
>> > Subject: [ESPResSo] parallel computing
>> > To:
address@hidden>> > Message-ID:
>> > <
address@hidden>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Hi,
>> >
>> > I'm very new to parallel computing and know very little about it so far.
>> I
>> > installed lam 7.1.4 on my computer and tried building espresso
>> > (--with-mpi=MPI option) but i got a lot of errors like this:
>> >
>> >
maggs.c:(.text+0x190be): undefined reference to `ompi_mpi_comm_world'
>> > maggs.c:(.text+0x190e4): undefined reference to `MPI_Irecv'
>> > maggs.c:(.text+0x19109): undefined reference to `ompi_mpi_comm_world'
>> > maggs.c:(.text+0x1953c): undefined reference to `ompi_mpi_comm_world'
>> > maggs.c:(.text+0x19542): undefined reference to `ompi_mpi_op_sum'
>> > maggs.c:(.text+0x19547): undefined reference to `ompi_mpi_double'
>> > maggs.c:(.text+0x19561): undefined reference to `MPI_Allreduce'
>> > maggs.c:(.text+0x198e8): undefined reference to `ompi_mpi_comm_world'
>> > maggs.c:(.text+0x198ee): undefined reference to `ompi_mpi_op_max'
>> > maggs.c:(.text+0x198f3): undefined reference to `ompi_mpi_double'
>> > maggs.c:(.text+0x1990d): undefined reference to `MPI_Allreduce'
>> > maggs.c:(.text+0x19ca7): undefined reference to
`ompi_mpi_comm_world'
>> > maggs.c:(.text+0x19cad): undefined reference to `ompi_mpi_op_sum'
>> > maggs.c:(.text+0x19cb2): undefined reference to `ompi_mpi_double'
>> > maggs.c:(.text+0x19cbc): undefined reference to `MPI_Allreduce'
>> > maggs.o: In function `Maggs_init':
>> > maggs.c:(.text+0x1a3c7): undefined reference to `ompi_mpi_comm_world'
>> > maggs.c:(.text+0x1a3cd): undefined reference to `ompi_mpi_op_sum'
>> > maggs.c:(.text+0x1a3d2): undefined reference to `ompi_mpi_double'
>> > maggs.c:(.text+0x1a3dc): undefined reference to `MPI_Reduce'
>> > maggs.o: In function `prepare_surface_planes':
>> > maggs.c:(.text+0x4915): undefined reference to `MPI_Type_commit'
>> >
>> > I also tried installing openmpi but got the same...
>> > I was wondering if anyone could help me to make parallel computing
work,
>> or
>> > maybe show me the manual of how to do this. Any help would be really
>> > appreciated because I don't even know where to start.
>> > I was thinking first to make both CPU's on my computer work together and
>> > then try running on several computers.
>> >
>> > Thanks a lot,
>> > Mikheil Azatov
>> > University of Maryland
>> > -------------- next part --------------
>> > An HTML attachment was scrubbed...
>> > URL:
>> >
>> http://fias.uni-frankfurt.de/pipermail/espresso/attachments/20100804/cba5a6dc/attachment-0001.htm>>
>>
>
-------------- next part --------------
An HTML attachment was
scrubbed...
URL: <http://fias.uni-frankfurt.de/pipermail/espresso/attachments/20100809/0322d6fe/attachment.htm>------------------------------
_______________________________________________
ESPResSo mailing list
address@hiddenhttps://fias.uni-frankfurt.de/mailman/listinfo/espressoEnd of ESPResSo Digest, Vol 39, Issue 6
***************************************