AMBER Archive (2008)

Subject: RE: AMBER: Error while compiling Amber

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Feb 09 2008 - 13:40:41 CST

Hi Lili,
 
It looks like /usr/bin/env is missing on your system. Likely it was never
installed. On my machine that is a link:
 
[11:34][caffeine:0.96][rcw:sander]$ ls -la /usr/bin/env
lrwxrwxrwx 1 root root 13 Jan 17 12:47 /usr/bin/env -> ../../bin/env
 
so env just points to /bin/env
 
Querying this file with rpm (since I am running RHEL4.0) gives:
 
[11:33][caffeine:0.91][rcw:sander]$ rpm -fq /usr/bin/env
coreutils-5.2.1-31.7
 
So it appears that /usr/bin/env is part of coreutils. I suspect this may be
missing on your machine or something is wrong with the installation. If you
are running RedHat or something similar which has rpm you can check what
version of coreutils is installed with:
 
[11:35][caffeine:1.02][rcw:bin]$ rpm -q coreutils
coreutils-5.2.1-31.7
 
The thing that is strange is that this is such a basic set of utils with
things like cat, head, tail etc I find it amazing that you wouldn't have it
installed. You could try to find where env is on your machine and create the
relevant link to it in /usr/bin/. Try 'which env'.
 
Failing that if you don't have env anywhere on your system you could try
getting the latest coreutils and reinstalling it.
 
Good luck,
 
Ross
 
/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

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be read every day, and should not be used for urgent or sensitive issues.
 

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Lili Peng
Sent: Saturday, February 09, 2008 11:12
To: amber_at_scripps.edu
Subject: Re: AMBER: Error while compiling Amber

Hi Ross,

Thanks for your suggestion. I did look into the README of MPICH2
(http://www.mcs.anl.gov/research/projects/mpich2/documentation/files/mpich2-
doc-README.txt) and tried to set up the daemon for MPD:

$ export PATH="/nas/lpeng/src/mpich2-1.0.6p1/bin"
$ which mpd
/nas/lpeng/src/mpich2-1.0.6p1/bin/mpd
$ which mpiexec
/nas/lpeng/src/mpich2-1.0.6p1/bin/mpiexec
$ which mpirun
/nas/lpeng/src/mpich2-1.0.6p1/bin/mpirun

Everything looks fine until I try to ring up the MPD:
$ mpd &
[1] 13151
/usr/bin/env: python2.4: No such file or directory
[1]+ Exit 127 mpd

What happened? why is it trying to access the env subdirectory, which
doesn't even exist bin?

Any leads on your behalf would be appreciated.

Thank you,
Lili

On 09/02/2008, Ross Walker <ross_at_rosswalker.co.uk> wrote:

Hi Lili,
 
You should check the manual for mpich2 - this version of mpi requires a
demon to be running (in this case called MPD) on all of the nodes on which
you want the code to run. This typically means setting up a machine file or
equivalent that is read by mpd.
 
If you just want to run this on the local machine to which you are logged in
then you can try.
 
mpd &
export DO_PARALLEL='mpirun =np 4'
make test.parallel
 
All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Lili Peng
Sent: Friday, February 08, 2008 17:52
To: amber_at_scripps.edu
Subject: Re: AMBER: Error while compiling Amber

Hi Dr. Case,
 
Thank you for your help. I added the parser.c file, and the serial
compilation of AMBER worked.
 
... Though I have another problem now. It's about compiling Sander in
parallel. Although I've searched the mailing list archives extensively,
none of what's been discussed addresses the issue. It has to do with the
make install function, and I'm trying to do a test run of sander. I have
already compiled my MPI library (the MPICH2 version). Here's my input code
(in bold) and the errors:
 
$ export AMBERHOME="/nas/lpeng/src/amber9"
$ export MPI_HOME="/nas/lpeng/opt"
$ export CC=icc
$ export FC=ifort
$ ./configure --prefix=/nas/lpeng/opt CC=$CC FC=$FC
$ make
$ make install
$ ./configure -mpich2 -p4 -static ifort_ia32
$ make parallel
 
... and Amber 9 was compiled successfully. Following the compiling
instructions, I continued on..
 
$ export DO_PARALLEL="/nas/lpeng/src/mpich2-1.0.6p1/bin/mpirun -np 4"
$ make test.sander
 
Then I get the error:
 
make: *** No rule ot make target 'test.sander'. Stop.
 
I also tried:
 
$ make test.parallel
 
..and receive in response:
 
export TESTsander=/nas/lpeng/src/amber9/exe/sander.MPI/exe/sander.MPI; make
test.sander.BASIC
make[1]: Entering directory `/nas/lpeng/src/amber9/test'
cd dmp; ./Run.dmp
This test not set up for parallel
 cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
 cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
mpiexec_granite.ucsd.edu: cannot connect to local mpd
(/tmp/mpd2.console_lpeng); possible causes:
  1. no mpd is running on this host
  2. an mpd is running but was started without a "console" (-n option)
In case 1, you can start an mpd on this host with:
    mpd &
and you will be able to run jobs just on this host.
For more details on starting mpds on a set of hosts, see
the MPICH2 Installation Guide.
  ./Run.cytosine: Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/nas/lpeng/src/amber9/test'
make: *** [test.sander.BASIC.MPI] Error 2
 
Do you have any leads on what is causing this to occur? Any input from your
end would be greatly appreciated.
 
Sincerely,
Lili
 
 
On 07/02/2008, David A. Case <case_at_scripps.edu> wrote:

On Thu, Feb 07, 2008, Lili Peng wrote:
>
>
> *$ ./configure -p4 ifort_x86_64*

What kind of machine are you compiling on? On the one hand, you say "-p4"
(which is for Pentium IV), yet you also say x86_64, which is a very
different
type of architecture.

Typing "uname -m" should give you the information you need. Then choose the
correct options.

>
> *$ ./configure -p4 ifort_ia32 *
> yacc parser.y
> make[2]: execvp: yacc: Permission denied

It looks like you got a lot further this time, so my guess is that you are
on
an ia32 (aka i386 aka i686) system. You should see that sander and lots of
other programs have been compiled. For the above problem:

First, try "which yacc" and try to find out if it exists, and if so, why
   you are getting permission denied.

Second, try "which bison": if it looks like you have permissions to run
bison,
add the line

YACC = bison -y

to your config.h file (in $AMBERHOME/src).

Or, if neither work, put the attached parser.c file in
$AMBERHOME/src/leap/src/leap, and try again.

....dac

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