You will have to recompile everything:<br>make clean<br>make<br><br>You still have references to lam in your libmd_mpi.so<br><br>Roland<br><br><div class="gmail_quote">On Tue, Mar 3, 2009 at 3:03 PM, Manik Mayur <span dir="ltr"><<a href="mailto:manik.mayur@gmail.com">manik.mayur@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><br><div class="gmail_quote"><div class="im">On Wed, Mar 4, 2009 at 1:18 AM, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
you will have to set<br><br>LD_LIBRARY_PATH to /home/openmpi/lib<br></blockquote><br></div>I have tried that.. the error still persists.<div><div><span id="q_11fce03352893a5d_3" class="h4">- Show quoted text -</span></div>
<div class="h5"><br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
use either setenv or export depending on your shell<br><br>Roland<br><br><div class="gmail_quote"><div><div></div><div>On Tue, Mar 3, 2009 at 2:35 PM, Manik Mayur <span dir="ltr"><<a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>this time upon executing :<div><br>./configure\<br>
--prefix /home/local/gromacs\<br>
--enable-mpi\<br>
--program-suffix="_mpi"\<br></div>
--disable-nice\<br> --enable-shared\<br>
MPICC=/home/openmpi/mpicc\<br><br>it exited with the following error:<br><br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_append'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `rw'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_deregister_object'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `nsend'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `dsend'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_trpoint'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamepub'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `mrev4'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `blktype'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_kexit'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_free'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigretry'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamedel'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodeid'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `rpdoom'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_next'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnameget'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `getrent'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `getntype'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksigsetretry'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `argvfree'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_errorstr'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `getroute'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `getnodes'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `kenter'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_ksignal'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_register_objects'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `bfselect'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lpattach'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `ldogetlinks'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_free'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_delete'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `kexit'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `nrecv'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `microsleep'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_init'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `bfrecv'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `show_help'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `next_prime'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `stoi'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `kinit'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_accept_tmout'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_open_srv_inet_stm'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `_kio'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `ttime'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_find'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_insert'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_init'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_insert'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiprobe'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_delete'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_set_buf_size'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_expand'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `al_find'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `getorigin'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrnamesweep'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `_lam_signal'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `sfh_sock_open_clt_inet_stm'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `rpstate'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `tprintf'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `kpause'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `ah_next'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `rev8'<br>
../mdlib/.libs/libmd_mpi.so: undefined reference to `argvadd'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `bfiselect'<br>../mdlib/.libs/libmd_mpi.so: undefined reference to `lam_rtrstore'<br>collect2: ld returned 1 exit status<br>
make[1]: *** [mdrun] Error 1<br><br>what is the problem now?</div></div><div><div><span>- Show quoted text -</span></div><div><div></div><div><div><br><br><div class="gmail_quote">On Wed, Mar 4, 2009 at 12:43 AM, Manik Mayur <span dir="ltr"><<a href="mailto:manik.mayur@gmail.com" target="_blank">manik.mayur@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><br><div class="gmail_quote"><div>On Wed, Mar 4, 2009 at 12:28 AM, Nicolas <span dir="ltr"><<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Manik Mayur a écrit :<div><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a> <mailto:<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a>>> wrote:<br>
<br>
Manik Mayur a écrit :<br>
<br>
Hi,<br>
<br>
If I have 2 mpi environments, namely LAM and openMPI, and I<br>
want gromacs to use openMPI of the two, what extra option<br>
should I pass during the ./configure step? In my case openMPI<br>
is installed locally(in my /home folder).<br>
<br>
Sorry, I've misunderstood your message. Anyway, I would first<br>
check twice the paths to the binaries in my script. Then, I would<br>
check my environment variables, especially PATH, LD_LIBRARY_PATH<br>
and LD_RUN_PATH. You might need to modify them to make sure any<br>
Lam-related stuff is loaded by default in your environment.<br>
<br>
<br>
ok, is there any specific option or environment variable through which I can make gromacs aware of openMPI and not LAM while installation? If I carry on the default --enable-mpi thing, upon executing the following:<br>
</blockquote></div>
Just a silly question: Did you recompile Gromacs with openMPI? If not, you should with the correct CPPFLAGS, LDFLAGS and MPICC. Typically, you should have something like:<br>
<br>
./configure\<br>
--prefix /home/local/gromacs\<br>
--enable-mpi\<br>
--program-suffix="_mpi"\<br>
--without-x\<br>
--disable-nice\<br>
MPICC=/path/to/mpicc\</blockquote></div><div><br>thanks, I think that is what I needed. Let me try and then I will let you know. <br><br></div><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
CC=/path/to/gcc<br>
CPPFLAGS=-I/path/to/fftw/include/\<br>
LDFLAGS=-L/path/to/fftw/lib/<br></blockquote>
<br></div>Why is FFTW necessary? In all my gromacs installations till now, I have avoided this package (out of ignorance).<div><div></div><div><br> <br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
mpicc is located in the bin/ directory of openMPI. gcc is the regular gcc installation (gcc 3). As I said, your issue is probably due to a path uncorrectly pointing to Lam. So check/modify your environment variables, especially the paths to loaded libraries.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>
<br>
$/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o eql_mpi.trr<br>
<br>
I get the following error:<br>
<br>
------------------------------------------------<br>
It seems that there is no lamd running on this host, which<br>
indicates<br>
that the LAM/MPI runtime environment is not operating. The<br>
LAM/MPI<br>
runtime environment is necessary for MPI programs to run (the MPI<br>
program tired to invoke the "MPI_Init" function).<br>
<br>
Please run the "lamboot" command the start the LAM/MPI runtime<br>
environment. See the LAM/MPI documentation for how to invoke<br>
"lamboot" across multiple machines.<br>
-----------------------------------------------------------------------------<br>
so it is like mdrun_mpi was configured with LAM and hence it is looking for it.<br>
<br>
I've tried to use a local installation of openMPI myself, but<br>
finally asked my sysadmin to install it for all users. I had many<br>
problems with libraries that couldn't be loaded properly.<br>
<br>
Cheers,<br>
Nicolas<br>
<br>
<br>
Thanks,<br>
Manik<br>
<br>
<br>
On Tue, Mar 3, 2009 at 10:58 PM, Nicolas <<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a><br></div>
<mailto:<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a>> <mailto:<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a><div><div></div><div><br>
<mailto:<a href="mailto:nsapay@ucalgary.ca" target="_blank">nsapay@ucalgary.ca</a>>>> wrote:<br>
<br>
Hi,<br>
<br>
As mentioned by the error message:<br>
<br>
<br>
Please run the "lamboot" command the start the LAM/MPI<br>
runtime<br>
<br>
Before using Lam, you have to boot it. In my scripts, I've got<br>
something like:<br>
<br>
lamboot -v $PBS_NODEFILE<br>
lamrun -v -np $NPROC mdrun mdargs<br>
lamhalt<br>
<br>
I don't use Lam often, though, you might need to use<br>
different Lam<br>
options.<br>
<br>
Nicolas<br>
<br>
Manik Mayur a écrit :<br>
<br>
Hi,<br>
<br>
I have till now successfully used openMPI and gromacs<br>
together. Recently I got a cluster where I tried to install<br>
openMPI and gromacs locally as I donot have root<br>
priviledges<br>
on it. But it turns out that it already has MPI<br>
environment on<br>
it (LAM) which I donot want to use (as the version is quite<br>
old.. the cluster still has gcc-3.2.3!).<br>
So after installing openMPI 1.3 and gromacs 4.0.4 on it<br>
(in my<br>
/home folder), I tried to execute:<br>
<br>
$/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s<br>
eql_mpi.tpr -o<br>
eql_mpi.trr<br>
<br>
It gives the following error:<br>
<br>
-----------------------------------------------------------------------------<br>
It seems that there is no lamd running on this host, which<br>
indicates<br>
that the LAM/MPI runtime environment is not operating. The<br>
LAM/MPI<br>
runtime environment is necessary for MPI programs to<br>
run (the MPI<br>
program tired to invoke the "MPI_Init" function).<br>
<br>
Please run the "lamboot" command the start the LAM/MPI<br>
runtime<br>
environment. See the LAM/MPI documentation for how to<br>
invoke<br>
"lamboot" across multiple machines.<br>
-----------------------------------------------------------------------------<br>
<br>
My question is - Why it still tries to look for LAM<br>
environment or lamd? I will be extremely thankful if<br>
somebody<br>
gives a hint.<br>
<br>
-Manik<br>
-- Graduate student<br>
Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>
IIT Kharagpur<br>
------------------------------------------------------------------------<br>
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<br>-- <br>Graduate student<br>Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>IIT Kharagpur<br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>
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<div class="h5"><br><br clear="all"><br>-- <br>Graduate student<br>Microfluidics Lab<br>
Dept. of Mechanical Engg.<br>IIT Kharagpur<br>
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865-241-1537, ORNL PO BOX 2008 MS6309<br>