Re: [gmx-users] g_sas

[David van der Spoel]

On 2010-04-04 07.13, Chih-Ying Lin wrote:


HI
THe command =>
g_sas_mpi -f 6LYZ-MD566500.xtc -s 6LYZ-MD566500.tpr -o
solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg



In the solvent-accessible-surface.xvg =>
@ s0 legend "Hydrophobic"
@ s1 legend "Hydrophilic"
@ s2 legend "Total"
@ s3 legend "D Gsolv"

What does "Hydrophobic" mean here?
What does "Hydrophilic" mean here?
Does "Total = Hydrophobic+Hydrophilic" ?
What does "D Gsolv" mean here?
How can Gromacs define "Hydrophobic atoms" and "Hydrophilic atoms" ?

DG solv is computed according to Eisenberg et al. See scree output for 
reference.


Hydrophobicity is determined from the charge of an atom, not a very good 
method maybe, there you can supply an index file to determine which 
residues are hydrophobic yourself.



What does the Area unit mean ? => "Area (nm\S2\N)"


How about square nanometer for an area?




Thank you
Lin




--
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
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[gmx-users] Re: configure error

[lina]

 Hello List,

for the record, the issue could be fixed by
regenerating the configure script with autoreconf version 2.13
(on a Debian (Squeeze) box).


Thanks,
Jerome BENOIT

 > Hello everyone,
 >
 > I tried to install gromacs on another cluster, after this,
 >
 > ./configure \
 >  --enable-shared \
 >  --enable-single \
 >  --enable-mpi \
 >  --program-suffix=_mpi \
 >  --enable-gsl
 >
 > there is a problem showing like this:
 >
 > gromacs checking size of void*... configure: error: cannot compute
 > sizeof (void*)
 >
 > the fftw has been installed successfully, and also gsl, but I do not
 > know why this happened? Some library, how can I fix this problem?
 
 > First, find the problem. Work out which of your configure options is 
 > causing the problem by omitting them systematically. Look in
config.log 
 > for more information about the error that is occurring. 
 > Mark
 > 

jgmbenoit-at+rezozer*dot_net


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[gmx-users] gromacs, lam and condor

[Hsin-Lin Chiang]

Hi,

I tried to use 4 and 8 CPUs.

There are about 6000 atoms in my system.

The interconnect of our computer is the network with speed 1Gb but not optical 
fiber.

I'm sorry for my poor English and I couldn't express well in my question.

Everytime I submitted the parallel job, the nodes assigned to mehave been 100% 
loading,

and the CPU source availble to me is less then 10%.

I think there is something wrong with my submit script or executable script,

and I post them in my previous message.

How should I correct my script?

Hsin-Lin

> Hi, 
> 
> how many CPUs do you try to use? How big is your system. What kind of 
> interconnect? Since you use condor probably some pretty slow interconnect. 
> Than you can't aspect it to work on many CPUs. If you want to use many CPUs 
> for MD you need a faster interconnect. 
> 
> Roland 
> 
> 2010/4/2 Hsin-Lin Chiang  
> 
> >  Hi, 
> > 
> > Do someone use gromacs, lam, and condor together here? 
> > I use gromacs with lam/mpi on condor system. 
> > Everytime I submit the parallel job. 
> > I got the node which is occupied before and the performance of each cpu is 
> > below 10%. 
> > How should I change the script? 
> > Below is one submit script and two executable script. 
> > 
> > condor_mpi: 
> >  
> > #!/bin/bash 
> > Universe = parallel 
> > Executable = ./lamscript 
> > machine_count = 8
> > output = md_$(NODE).out 
> > error = md_$(NODE).err 
> > log = md.log 
> > arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh 
> > +WantIOProxy = True 
> > should_transfer_files = yes 
> > when_to_transfer_output = on_exit 
> > Queue 
> > --- 
> > 
> > lamscript: 
> > --- 
> > #!/bin/sh 
> > 
> > _CONDOR_PROCNO=$_CONDOR_PROCNO 
> > _CONDOR_NPROCS=$_CONDOR_NPROCS 
> > _CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR 
> > 
> > SSHD_SH=`condor_config_val libexec` 
> > SSHD_SH=$SSHD_SH/sshd.sh 
> > 
> > CONDOR_SSH=`condor_config_val libexec` 
> > CONDOR_SSH=$CONDOR_SSH/condor_ssh 
> > 
> > # Set this to the bin directory of your lam installation 
> > # This also must be in your .cshrc file, so the remote side 
> > # can find it! 
> > export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4 
> > export PATH=${LAMDIR}/bin:${PATH} 
> > export LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib 
> > 
> > 
> > . $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS 
> > 
> > # If not the head node, just sleep forever, to let the 
> > # sshds run 
> > if [ $_CONDOR_PROCNO -ne 0 ] 
> > then 
> >                 wait 
> >                 sshd_cleanup 
> >                 exit 0 
> > fi 
> > 
> > EXECUTABLE=$1 
> > shift 
> > 
> > # the binary is copied but the executable flag is cleared. 
> > # so the script have to take care of this 
> > chmod +x $EXECUTABLE 
> > 
> > # to allow multiple lam jobs running on a single machine, 
> > # we have to give somewhat unique value 
> > export LAM_MPI_SESSION_SUFFIX=$$ 
> > export LAMRSH=$CONDOR_SSH 
> > # when a job is killed by the user, this script will get sigterm 
> > # This script have to catch it and do the cleaning for the 
> > # lam environment 
> > finalize() 
> > { 
> > sshd_cleanup 
> > lamhalt 
> > exit 
> > } 
> > trap finalize TERM 
> > 
> > CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact 
> > export $CONDOR_CONTACT_FILE 
> > # The second field in the contact file is the machine name 
> > # that condor_ssh knows how to use. Note that this used to 
> > # say "sort -n +0 ...", but -n option is now deprecated. 
> > sort < $CONDOR_CONTACT_FILE | awk '{print $2}' > machines 
> > 
> > # start the lam environment 
> > # For older versions of lam you may need to remove the -ssi boot rsh line 
> > lamboot -ssi boot rsh -ssi rsh_agent "$LAMRSH -x" machines 
> > 
> > if [ $? -ne 0 ] 
> > then 
> >         echo "lamscript error booting lam" 
> >         exit 1 
> > fi 
> > 
> > mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@ & 
> > 
> > CHILD=$! 
> > TMP=130 
> > while [ $TMP -gt 128 ] ; do 
> >         wait $CHILD 
> >         TMP=$?; 
> > done 
> > 
> > # clean up files 
> > sshd_cleanup 
> > /bin/rm -f machines 
> > 
> > # clean up lam 
> > lamhalt 
> > 
> > exit $TMP 
> >  
> > 
> > md.sh 
> >  
> > #!/bin/sh 
> > #running GROMACS 
> > /stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \ 
> > -s /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.tpr \ 
> > -e /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.edr \ 
> > -o /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.trr \ 
> > -g /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.log \ 
> > -c /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md/200ns.gro 
> > - 
> > 
> > 
> > Hsin-Lin 
 
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Re: [gmx-users] Potential Tables for user defined potentials

[Gareth Tribello]

Hi all

I have just been stuck on this very problem of user defined potentials.
 When I emailed this list I was asked if I could make notes on the solution
as this is a problem that seems to come up a lot.  Anyway, I will send the
notes to you separately Sikandar and would ask if anyone knows where should
put/send them if they are to be accessible to the user community?

Many thanks
Gareth

On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul  wrote:

>
>
> Sikandar Mashayak wrote:
>
>> Hi
>>
>> I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that
>> I need to use custom potential field parameters for fluid-fluid and
>> fluid-wall interactions.
>>
>> So my question is that, how can I use potential table approach to specify
>> fluid-fluid and fluid-wall interactions seperately?
>>
>>
> Start with the manual, section 6.7.2, and see the table*.xvg in the
> /share/top subdirectory of your Gromacs installation for examples.
>
> -Justin
>
>  Thanks
>> sikandar
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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Re: [gmx-users] Potential Tables for user defined potentials

[Sikandar Mashayak]

Hi
Gareth

Thanks for the notes on user defined potentials in GROMACS. I will go
through it and will send you the feedback after I get the simulation
results.


Thanks
sikandar

On Sun, Apr 4, 2010 at 11:27 AM, Gareth Tribello
wrote:

> Hi all
>
> I have just been stuck on this very problem of user defined potentials.
>  When I emailed this list I was asked if I could make notes on the solution
> as this is a problem that seems to come up a lot.  Anyway, I will send the
> notes to you separately Sikandar and would ask if anyone knows where should
> put/send them if they are to be accessible to the user community?
>
> Many thanks
> Gareth
>
>
> On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul  wrote:
>
>>
>>
>> Sikandar Mashayak wrote:
>>
>>> Hi
>>>
>>> I plan to do 'fluid in channel' simulations using GROMACS 4.0.7. For that
>>> I need to use custom potential field parameters for fluid-fluid and
>>> fluid-wall interactions.
>>>
>>> So my question is that, how can I use potential table approach to specify
>>> fluid-fluid and fluid-wall interactions seperately?
>>>
>>>
>> Start with the manual, section 6.7.2, and see the table*.xvg in the
>> /share/top subdirectory of your Gromacs installation for examples.
>>
>> -Justin
>>
>>  Thanks
>>> sikandar
>>>
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>
>
> --
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[gmx-users] DSSP=> how to edit .eps file

[Chih-Ying Lin]

Hi
With the following two commands,

do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg

xpm2ps -f secondary-structure.xpm -o secondary-structure.eps


With GIMP, i can see the secondary structure plot. The legend indicates the
color of different second structure is shown under the secondary-structure
plot.



One legend is half-shown. The picture of legend is cut.
How can I get that legend full-shown.

Thank you
Lin
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Re: [gmx-users] DSSP=> how to edit .eps file

[Justin A. Lemkul]

Chih-Ying Lin wrote:


Hi
With the following two commands,  


do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc 
secondary-structure.xvg

xpm2ps -f secondary-structure.xpm -o secondary-structure.eps


With GIMP, i can see the secondary structure plot. The legend indicates 
the color of different second structure is shown under the 
secondary-structure plot.




One legend is half-shown. The picture of legend is cut.
How can I get that legend full-shown.



The dimensions of the plot area are likely too small to accommodate the full 
legend.  As I said before, pass an .m2p file to xpm2ps to change the dimensions 
of the plot, data point size, etc.


-Justin


Thank you
Lin





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Potential Tables for user defined potentials

[Justin A. Lemkul]

Gareth Tribello wrote:

Hi all

I have just been stuck on this very problem of user defined potentials. 
 When I emailed this list I was asked if I could make notes on the 
solution as this is a problem that seems to come up a lot.  Anyway, I 
will send the notes to you separately Sikandar and would ask if anyone 
knows where should put/send them if they are to be accessible to the 
user community?


Yes, please post whatever pointers  you have to the list so it can be archived, 
and if you have time, create a How-To page on the Gromacs site.  In recent 
weeks, it seems that half of the questions asked are in regards to tabulated 
potentials.  It would be nice to have some help information accessible.


-Justin



Many thanks
Gareth

On Sun, Apr 4, 2010 at 3:47 AM, Justin A. Lemkul > wrote:




Sikandar Mashayak wrote:

Hi

I plan to do 'fluid in channel' simulations using GROMACS 4.0.7.
For that I need to use custom potential field parameters for
fluid-fluid and fluid-wall interactions.

So my question is that, how can I use potential table approach
to specify fluid-fluid and fluid-wall interactions seperately?


Start with the manual, section 6.7.2, and see the table*.xvg in the
/share/top subdirectory of your Gromacs installation for examples.

-Justin

Thanks
sikandar


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] g_sas

[Chih-Ying Lin]

Hi

g_sas computes hydrophobic, hydrophilic and total solvent accessible surface
area.

I chose => protein for calculation group
=> protein for output group

what does it define "hydrophobic solvent accessible surface area"?
=> does that, the surface area, enclose the hydrophobic atoms/residues?

what does it define "hydrophilic solvent accessible surface area"?
 => does that, the surface area, enclose the hydrophilic atoms/residues?


what does it define "total solvent accessible surface area"?
 => does that, the surface area, enclose the total surface of the protein?



I got hydrophobic SAS is  greater than hydrophilic SAS.
Isn't correct ?
I am supposing that hydrophobic atoms/residues are within the protein.
And, hydrophilic atoms/residues are on the surface of the protein.


Then, how can "hydrophobic SAS is  greater than hydrophilic SAS" ?

Thank you
Lin
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[gmx-users] g_sas

[Chih-Ying Lin]

Hi
>From David,
"If you select a
group consisting of a single residue in a protein the SAS will be
computed as if the rest of the protein is not there. Very useful when
you want to compute protein-protein interface areas."


=> therefore, if i select a group consisting of a single residue, which is
in the core of a protein, it is impossible that water penetrates into the
core of the protein so SAS is supposed to be zero.

=> However, after calculation with g_sas, the SAS_calculation of the single
residue residing in the core of the protein is NOT ZERO.

=> My understanding is that g_sas returns the surface area of the single
residue and it does not matter where the single residue locates.
 right?

=> The single residue can locate in the core of the protein or on the
surface of the protein. The g_sas calculation for the single residue will
not make a huge difference unless the single residue deforms/ twists .
 on the surface or in the core of the protein,right ?


=> How to compute protein-protein interface area?

=> In the protein + ligands + water system, I want to compute protein-ligand
interface, protein-water interface, and ligand-water interface separately.
 => How?


=> in the protein + water system, g_sas computes the total SAS fluctuating
between   88  and  144  (angstrom_squares)
=> does it make sense ?
=> I don't think that protein will swell 50 % plus in the pure water.
=> But why ??


=> How to calculate the surface area of a micelle ?

Thank you
Lin


















>> Hi
>> The command
>> g_sas => Select a group for calculation of surface and a group for output
>>
>>
>> What is the difference between "a group for calculation of surface"
>> and "a group for output"?
>
> Please consult the documentation. From g_sas -h:
>
> "The program will ask for a group for the surface calculation and a
> group for the output. The calculation group should always consists of
> all the non-solvent atoms in the system. The output group can be the
> whole or part of the calculation group."
>
Actually this documentation is not correct.

The calculation group are those atoms taken into account in the
computation, whether or not they are solvent accessible. If you select a
group consisting of a single residue in a protein the SAS will be
computed as if the rest of the protein is not there. Very useful when
you want to compute protein-protein interface areas.

> -Justin
>
>> Thank you
>> Lin
>>
>


--
David.
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[gmx-users] DSSP=> how to edit .eps file

[Chih-Ying Lin]

HI
How to pass an .m2p file to xpm2ps to change the dimensions
of the plot, data point size, etc. ???

Thank you

Lin




Chih-Ying Lin wrote:
>
> Hi
> With the following two commands,
>
> do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg
>
> xpm2ps -f secondary-structure.xpm -o secondary-structure.eps
>
>
> With GIMP, i can see the secondary structure plot. The legend indicates
> the color of different second structure is shown under the
> secondary-structure plot.
>
>
>
> One legend is half-shown. The picture of legend is cut.
> How can I get that legend full-shown.
>

The dimensions of the plot area are likely too small to accommodate the full
legend.  As I said before, pass an .m2p file to xpm2ps to change the
dimensions
of the plot, data point size, etc.

-Justin

> Thank you
> Lin
>
>
>
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Re: [gmx-users] DSSP=> how to edit .eps file

[Justin A. Lemkul]

Chih-Ying Lin wrote:

HI
How to pass an .m2p file to xpm2ps to change the dimensions
of the plot, data point size, etc. ???


Use the -di flag of xpm2ps.

http://manual.gromacs.org/current/online/m2p.html

-Justin



Thank you

Lin




Chih-Ying Lin wrote:


 Hi
 With the following two commands,

 do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc 

secondary-structure.xvg


 xpm2ps -f secondary-structure.xpm -o secondary-structure.eps


 With GIMP, i can see the secondary structure plot. The legend indicates
 the color of different second structure is shown under the
 secondary-structure plot.



 One legend is half-shown. The picture of legend is cut.
 How can I get that legend full-shown.



The dimensions of the plot area are likely too small to accommodate the full
legend.  As I said before, pass an .m2p file to xpm2ps to change the 
dimensions

of the plot, data point size, etc.

-Justin


 Thank you
 Lin







--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] gromacs, lam and condor

[Oliver Stueker]

Hi Hsin-Lin,

As Mark answered already yesterday:
1) 1Gb Ethernet is not fast enough for more than 2 or maximum 4 CPUs.
(and if each process of mdrun has to wait ~90% of the time to get data
from the others, then you result in just 10% load, right? )

2) telling from the line:
>> > /stathome/jiangsl/soft/gromacs-4.0.5/bin/mdrun_mpi_d \
you are using a double precision of gromacs that slows things down and
is only of use in very special cases. use mdrun_mpi instead.

3) your system is just 6000 atoms small, I would rather run such a
small system on one dual-core system (so max 2 CPU's)
 I don't think the system will scale well on more CPU's

And in case there's really something wrong with condor and has nothing
to do with gromacs then this is the wrong mailing-list anyway.


Oliver

2010/4/4 Hsin-Lin Chiang :
> Hi,
>
>
>
> I tried to use 4 and 8 CPUs.
>
> There are about 6000 atoms in my system.
>
> The interconnect of our computer is the network with speed 1Gb but not
> optical fiber.
>
>
>
> I'm sorry for my poor English and I couldn't express well in my question.
>
> Everytime I submitted the parallel job, the nodes assigned to mehave been
> 100% loading,
>
> and the CPU source availble to me is less then 10%.
>
> I think there is something wrong with my submit script or executable script,
>
> and I post them in my previous message.
>
> How should I correct my script?
>
>
>
> Hsin-Lin
>
>
>> Hi,
>>
>> how many CPUs do you try to use? How big is your system. What kind of
>> interconnect? Since you use condor probably some pretty slow interconnect.
>> Than you can't aspect it to work on many CPUs. If you want to use many
>> CPUs
>> for MD you need a faster interconnect.
>>
>> Roland
>>
>> 2010/4/2 Hsin-Lin Chiang 
>>
>> >  Hi,
>> >
>> > Do someone use gromacs, lam, and condor together here?
>> > I use gromacs with lam/mpi on condor system.
>> > Everytime I submit the parallel job.
>> > I got the node which is occupied before and the performance of each cpu
>> > is
>> > below 10%.
>> > How should I change the script?
>> > Below is one submit script and two executable script.
>> >
>> > condor_mpi:
>> > 
>> > #!/bin/bash
>> > Universe = parallel
>> > Executable = ./lamscript
>> > machine_count = 8
>> > output = md_$(NODE).out
>> > error = md_$(NODE).err
>> > log = md.log
>> > arguments = /stathome/jiangsl/simulation/gromacs/2OMP/2OMP_1_1/md.sh
>> > +WantIOProxy = True
>> > should_transfer_files = yes
>> > when_to_transfer_output = on_exit
>> > Queue
>> > ---
>> >
>> > lamscript:
>> > ---
>> > #!/bin/sh
>> >
>> > _CONDOR_PROCNO=$_CONDOR_PROCNO
>> > _CONDOR_NPROCS=$_CONDOR_NPROCS
>> > _CONDOR_REMOTE_SPOOL_DIR=$_CONDOR_REMOTE_SPOOL_DIR
>> >
>> > SSHD_SH=`condor_config_val libexec`
>> > SSHD_SH=$SSHD_SH/sshd.sh
>> >
>> > CONDOR_SSH=`condor_config_val libexec`
>> > CONDOR_SSH=$CONDOR_SSH/condor_ssh
>> >
>> > # Set this to the bin directory of your lam installation
>> > # This also must be in your .cshrc file, so the remote side
>> > # can find it!
>> > export LAMDIR=/stathome/jiangsl/soft/lam-7.1.4
>> > export PATH=${LAMDIR}/bin:${PATH}
>> > export
>> > LD_LIBRARY_PATH=/lib:/usr/lib:$LAMDIR/lib:.:/opt/intel/compilers/lib
>> >
>> >
>> > . $SSHD_SH $_CONDOR_PROCNO $_CONDOR_NPROCS
>> >
>> > # If not the head node, just sleep forever, to let the
>> > # sshds run
>> > if [ $_CONDOR_PROCNO -ne 0 ]
>> > then
>> >                 wait
>> >                 sshd_cleanup
>> >                 exit 0
>> > fi
>> >
>> > EXECUTABLE=$1
>> > shift
>> >
>> > # the binary is copied but the executable flag is cleared.
>> > # so the script have to take care of this
>> > chmod +x $EXECUTABLE
>> >
>> > # to allow multiple lam jobs running on a single machine,
>> > # we have to give somewhat unique value
>> > export LAM_MPI_SESSION_SUFFIX=$$
>> > export LAMRSH=$CONDOR_SSH
>> > # when a job is killed by the user, this script will get sigterm
>> > # This script have to catch it and do the cleaning for the
>> > # lam environment
>> > finalize()
>> > {
>> > sshd_cleanup
>> > lamhalt
>> > exit
>> > }
>> > trap finalize TERM
>> >
>> > CONDOR_CONTACT_FILE=$_CONDOR_SCRATCH_DIR/contact
>> > export $CONDOR_CONTACT_FILE
>> > # The second field in the contact file is the machine name
>> > # that condor_ssh knows how to use. Note that this used to
>> > # say "sort -n +0 ...", but -n option is now deprecated.
>> > sort < $CONDOR_CONTACT_FILE | awk '{print $2}' > machines
>> >
>> > # start the lam environment
>> > # For older versions of lam you may need to remove the -ssi boot rsh
>> > line
>> > lamboot -ssi boot rsh -ssi rsh_agent "$LAMRSH -x" machines
>> >
>> > if [ $? -ne 0 ]
>> > then
>> >         echo "lamscript error booting lam"
>> >         exit 1
>> > fi
>> >
>> > mpirun C -ssi rpi usysv -ssi coll_smp 1 $EXECUTABLE $@ &
>> >
>> > CHILD=$!
>> > TMP=130
>> > while [ $TMP -gt 128 ] ; do
>> >         wait $CHILD
>> >         TMP=$?;
>> > done
>> >
>> > # clean up files
>> > sshd_cleanup
>> > /bin/rm -f machines
>> >
>> > # clean up lam