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Subject: Re: [OMPI users] ssh MPi and program tests
From: Francesco Pietra (chiendarret_at_[hidden])
Date: 2009-04-07 09:56:32


Hi Jody:
I should only blame myself. Gustavo's indications were clear. Still, I
misunderstood them.

Since I am testing on one node (where everything is there)

mpirun -host deb64 -n 4 connectivity_c

Connectivity test on 4 processes PASSED

thanks
francesco

On Tue, Apr 7, 2009 at 12:27 PM, jody <jody.xha_at_[hidden]> wrote:
> Hi
>
> What are the options "-deb64" and "-1" you are passing to mpirun:
>> /usr/local/bin/mpirun -deb64 -1 connectivity_c 2>&1 | tee n=1.connectivity.out
>
> I don't think these are legal options for mpirun (at least they don't
> show up in `man mpirun`).
> And i think you should add a "-n 4" (for 4 processors)
> Furthermore, if you want to specify a host, you have to add "-host hostname1"
> if you want to specify several hosts you have to add "-host
> hostname1,hostname2,hostname3"  (no spaces around the commas)
>
> Jody
>
>
> On Tue, Apr 7, 2009 at 11:39 AM, Francesco Pietra <chiendarret_at_[hidden]> wrote:
>> Hi Gus:
>> I should have set clear at the beginning that on the Zyxel router
>> (connected to Internet by dynamic IP afforded by the provider)  there
>> are three computers. Their host names:
>>
>> deb32 (desktop debian i386)
>>
>> deb64 (multisocket debian amd 64 lenny)
>>
>> tya64 (multisocket debian amd 64 lenny)
>>
>> The three are ssh passwordless interconnected from the same user
>> (myself). I never established connections as root user because I have
>> direct access to all tree computers. So, if I slogin as user,
>> passwordless connection is established. If I try to slogin as root
>> user, it says that the authenticity of the host to which I intended to
>> connect can't be established, RSA key fingerprint .. Connect?
>>
>> Moreover, I appended to the pub keys know to deb64 those that deb64
>> had sent to either deb32 or tya64. Whereby, when i command.
>>
>> With certain programs (conceived for batch run), the execution on
>> deb64 is launched from deb32.
>>
>> ssh 192.168.#.## date (where the numbers stand for hostname)
>>
>>
>> I copied /examples to my deb64 home, chown to me, compiled as user and
>> run as user "connectivity".  (I have not compild in the openmpi
>> directory as this is to root user, while ssh has been adjusted for me
>> as user.
>>
>> Running as user in my home
>>
>> /usr/local/bin/mpirun -deb64 -1 connectivity_c 2>&1 | tee n=1.connectivity.out
>>
>> it asked to add the host (himself) to the list on known hosts (on
>> repeating the command, that was no more asked). The unabridged output:
>>
>> ===========
>> [deb64:03575] procdir: /tmp/openmpi-sessions-francesco_at_deb64_0/38647/0/0
>> [deb64:03575] jobdir: /tmp/openmpi-sessions-francesco_at_deb64_0/38647/0
>> [deb64:03575] top: openmpi-sessions-francesco_at_deb64_0
>> [deb64:03575] tmp: /tmp
>> [deb64:03575] mpirun: reset PATH:
>> /usr/local/bin:/usr/local/mcce/bin:/opt/intel/cce/10.1.015/bin:/opt/intel/fce/10.1.015/bin:/home/francesco/gmmx06:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/local/amber10/exe:/usr/local/dock6/bin
>> [deb64:03575] mpirun: reset LD_LIBRARY_PATH:
>> /usr/local/lib:/opt/intel/mkl/10.0.1.014/lib/em64t:/opt/intel/cce/10.1.015/lib:/opt/intel/fce/10.1.015/lib:/usr/local/lib:/opt/acml4.1.0/gfortran64_mp_int64/lib
>> [deb64:03583] procdir: /tmp/openmpi-sessions-francesco_at_deb64_0/38647/0/1
>> [deb64:03583] jobdir: /tmp/openmpi-sessions-francesco_at_deb64_0/38647/0
>> [deb64:03583] top: openmpi-sessions-francesco_at_deb64_0
>> [deb64:03583] tmp: /tmp
>> [deb64:03575] [[38647,0],0] node[0].name deb64 daemon 0 arch ffc91200
>> [deb64:03575] [[38647,0],0] node[1].name deb64 daemon 1 arch ffc91200
>> [deb64:03583] [[38647,0],1] node[0].name deb64 daemon 0 arch ffc91200
>> [deb64:03583] [[38647,0],1] node[1].name deb64 daemon 1 arch ffc91200
>> --------------------------------------------------------------------------
>> mpirun was unable to launch the specified application as it could not
>> find an executable:
>>
>> Executable: -e
>> Node: deb64
>>
>> while attempting to start process rank 0.
>> --------------------------------------------------------------------------
>> [deb64:03575] sess_dir_finalize: job session dir not empty - leaving
>> [deb64:03575] sess_dir_finalize: proc session dir not empty - leaving
>> orterun: exiting with status -123
>> [deb64:03583] sess_dir_finalize: job session dir not empty - leaving
>> =========================
>>
>> I have changed the command, setting 4 for n and giving the full path
>> to the executable "connectivity_c" at no avail. I do not understand
>> the message "Executable: -e" in the out file and I feel myself stupid
>> enough in this circumstance.
>>
>> The ssh is working for slogin and ssh to deb 64 date gives the date
>> passwordless, both before and after the "connectivity" run. i.e.,
>> deb64 knew, and knows, itself.
>>
>> The output of ompi_info between xxxxxxxxxx should probably clarify
>> your other questions.
>>
>> xxxxxxxxxxxxxxxxxxx
>>                 Package: Open MPI root_at_deb64 Distribution
>>                Open MPI: 1.3.1
>>   Open MPI SVN revision: r20826
>>   Open MPI release date: Mar 18, 2009
>>                Open RTE: 1.3.1
>>   Open RTE SVN revision: r20826
>>   Open RTE release date: Mar 18, 2009
>>                    OPAL: 1.3.1
>>       OPAL SVN revision: r20826
>>       OPAL release date: Mar 18, 2009
>>            Ident string: 1.3.1
>>                  Prefix: /usr/local
>>  Configured architecture: x86_64-unknown-linux-gnu
>>          Configure host: deb64
>>           Configured by: root
>>           Configured on: Fri Apr  3 23:03:30 CEST 2009
>>          Configure host: deb64
>>                Built by: root
>>                Built on: Fri Apr  3 23:12:28 CEST 2009
>>              Built host: deb64
>>              C bindings: yes
>>            C++ bindings: yes
>>      Fortran77 bindings: yes (all)
>>      Fortran90 bindings: yes
>>  Fortran90 bindings size: small
>>              C compiler: gcc
>>     C compiler absolute: /usr/bin/gcc
>>            C++ compiler: g++
>>   C++ compiler absolute: /usr/bin/g++
>>      Fortran77 compiler: /opt/intel/fce/10.1.015/bin/ifort
>>  Fortran77 compiler abs:
>>      Fortran90 compiler: /opt/intel/fce/10.1.015/bin/ifort
>>  Fortran90 compiler abs:
>>             C profiling: yes
>>           C++ profiling: yes
>>     Fortran77 profiling: yes
>>     Fortran90 profiling: yes
>>          C++ exceptions: no
>>          Thread support: posix (mpi: no, progress: no)
>>           Sparse Groups: no
>>  Internal debug support: no
>>     MPI parameter check: runtime
>> Memory profiling support: no
>> Memory debugging support: no
>>         libltdl support: yes
>>   Heterogeneous support: no
>>  mpirun default --prefix: no
>>         MPI I/O support: yes
>>       MPI_WTIME support: gettimeofday
>> Symbol visibility support: yes
>>   FT Checkpoint support: no  (checkpoint thread: no)
>>           MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.3.1)
>>           MCA paffinity: linux (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA carto: file (MCA v2.0, API v2.0, Component v1.3.1)
>>           MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.3.1)
>>           MCA maffinity: libnuma (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA timer: linux (MCA v2.0, API v2.0, Component v1.3.1)
>>         MCA installdirs: env (MCA v2.0, API v2.0, Component v1.3.1)
>>         MCA installdirs: config (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA dpm: orte (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.3.1)
>>           MCA allocator: basic (MCA v2.0, API v2.0, Component v1.3.1)
>>           MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: basic (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: inter (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: self (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: sm (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: sync (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA coll: tuned (MCA v2.0, API v2.0, Component v1.3.1)
>>                  MCA io: romio (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA mpool: fake (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA mpool: sm (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA pml: cm (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA pml: v (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA bml: r2 (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA rcache: vma (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA btl: self (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA btl: sm (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA btl: tcp (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA topo: unity (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA osc: rdma (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA iof: hnp (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA iof: orted (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA iof: tool (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA oob: tcp (MCA v2.0, API v2.0, Component v1.3.1)
>>                MCA odls: default (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA ras: slurm (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA rmaps: round_robin (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA rml: oob (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA routed: binomial (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA routed: direct (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA routed: linear (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA plm: rsh (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA plm: slurm (MCA v2.0, API v2.0, Component v1.3.1)
>>               MCA filem: rsh (MCA v2.0, API v2.0, Component v1.3.1)
>>              MCA errmgr: default (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA ess: env (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA ess: hnp (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA ess: singleton (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA ess: slurm (MCA v2.0, API v2.0, Component v1.3.1)
>>                 MCA ess: tool (MCA v2.0, API v2.0, Component v1.3.1)
>>             MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.3.1)
>>             MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.3.1)
>> xxxxxxxxxxxxxxxxxxxxxxxxxx
>>
>> thanks
>> francesco
>>
>> On Mon, Apr 6, 2009 at 11:03 PM, Gus Correa <gus_at_[hidden]> wrote:
>>> Hi Francesco
>>>
>>>
>>> See answers inline.
>>>
>>> Francesco Pietra wrote:
>>>>
>>>> Hi Gus:
>>>> Partial quick answers below. I have reestablished the ssh connection
>>>> so that tomorrow I'll run the tests. Everything that relates to
>>>> running amber is on the "parallel computer", where I have access to
>>>> everything.
>>>>
>>>> On Mon, Apr 6, 2009 at 7:53 PM, Gus Correa <gus_at_[hidden]> wrote:
>>>>>
>>>>> Hi Francesco, list
>>>>>
>>>>> Francesco Pietra wrote:
>>>>>>
>>>>>> On Mon, Apr 6, 2009 at 5:21 PM, Gus Correa <gus_at_[hidden]>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Francesco
>>>>>>>
>>>>>>> Did you try to run examples/connectivity_c.c,
>>>>>>> or examples/hello_c.c before trying amber?
>>>>>>> They are in the directory where you untarred the OpenMPI tarball.
>>>>>>> It is easier to troubleshoot
>>>>>>> possible network and host problems
>>>>>>> with these simpler programs.
>>>>>>
>>>>>> I have found the "examples". Should they be compiled? how? This is my
>>>>>> only question here.
>>>>>
>>>>> cd examples/
>>>>> /full/path/to/openmpi/bin/mpicc -o connectivity_c connectivity_c.c
>>>>>
>>>>> Then run it with, say:
>>>>>
>>>>> /full/path/to/openmpi/bin/mpirun -host {whatever_hosts_you_want}
>>>>> -n {as_many_processes_you_want} connectivity_c
>>>>>
>>>>> Likewise for hello_c.c
>>>>>
>>>>>> What's below is info. Although amber parallel
>>>>>> would have not compiled with faulty openmpi, I'll run openmpi tests as
>>>>>> soon as I understand how.
>>>>>>
>>>>>>> Also, to avoid confusion,
>>>>>>> you may use a full path name to mpirun,
>>>>>>> in case you have other MPI flavors in your system.
>>>>>>> Often times the mpirun your path is pointing to is not what you
>>>>>>> may think it is.
>>>>>>
>>>>>> which mpirun
>>>>>> /usr/local/bin/mpirun
>>>>>
>>>>> Did you install OpenMPI on /usr/local ?
>>>>> When you do "mpirun -help", do you see "mpirun (Open MPI) 1.3"?
>>>>
>>>> mpirun -help
>>>> mpirun (Open MPI) 1.3.1
>>>> on the 1st line, then follow the options
>>>
>>> Ok, it looks like you installed OpenMPI 1.3.1 with the default
>>> "--prefix" which is /usr/local.
>>>
>>>>
>>>>
>>>>> How about the output of "orte_info" ?
>>>>
>>>> orte_info was not installed. See below what has been installed.
>>>>
>>>
>>> Sorry, my fault.
>>> I meant ompi_info (not orte_info).
>>> Please try ompi_info or "ompi_info --config".
>>> It will tell you the compilers used to build OpenMPI, etc.
>>>
>>> I presume all of this is being done in the "parallel computer",
>>> i.e., in one of the AMD64 Debian systems, right?
>>>
>>>>
>>>>> Does it show your Intel compilers, etc?
>>>>
>>>> I guess so, otherwise amber would have not been compiled, but I don't
>>>> know the commands to prove it. The intel compilers are on the path:
>>>> /opt/intel/cce/10.1.015/bin:/opt/intel/fce/10.1.015/bin and the mkl
>>>> are sourced in .bashrc.
>>>>
>>>
>>> Again, all in the AMD64 system, right?
>>>
>>>>> I ask because many Linux distributions come with one or more flavors
>>>>> of MPI (OpenMPI, MPICH, LAM, etc), some compilers also do (PGI for
>>>>> instance), some tools (Intel MKL?) may also have their MPI,
>>>>> and you end up with a bunch of MPI commands
>>>>> on your path that may produce a big mixup.
>>>>> This is a pretty common problem that affect new users on this list,
>>>>> on the MPICH list, on clustering lists, etc.
>>>>> The errors messages often don't help find the source of the problem,
>>>>> and people spend a lot of time trying to troubleshoot network,
>>>>> etc, when is often just a path problem.
>>>>>
>>>>> So, this is why when you begin, you may want to use full path
>>>>> names, to avoid confusion.
>>>>> After the basic MPI functionality is working,
>>>>> then you can go and fix your path chain,
>>>>> and rely on your path chain.
>>>>>
>>>>>> there is no other accessible MPI (one application, DOT2, has mpich but
>>>>>> it is a static compilation; DOT2 parallelizatuion requires thar the
>>>>>> computer knows itself, i.e." ssh hostname date" should afford the date
>>>>>> passwordless. The reported issues in testing amber have destroyed this
>>>>>> situation: now deb64 has port22 closed, evem to itself.
>>>>>>
>>>>> Have you tried to reboot the master node, to see if it comes back
>>>>> to the original ssh setup?
>>>>> You need ssh to be functional to run OpenMPI code,
>>>>> including the tests above.
>>>>>
>>>>>>> I don't know if you want to run on amd64 alone (master node?)
>>>>>>> or on a cluster.
>>>>>>> In any case, you may use a list of hosts
>>>>>>> or a hostfile on the mpirun command line,
>>>>>>> to specify where you want to run.
>>>>>>
>>>>>> With amber I use the parallel computer directly and the amber
>>>>>> installation is chown to me. The ssh connection, in this case, only
>>>>>> serves to get file from. or send files to, my desktop.
>>>>>>
>>>>> It is unclear to me what you mean by "the parallel computer directly".
>>>>> Can you explain better which computers are in this game?
>>>>> Your desktop and a cluster perhaps?
>>>>> Are they both Debian 64 Linux?
>>>>> Where do you compile the programs?
>>>>> Where do you want to run the programs?
>>>>>
>>>>>> In my .bashrc:
>>>>>>
>>>>>> (for amber)
>>>>>> MPI_HOME=/usr/local
>>>>>> export MPI_HOME
>>>>>>
>>>>>> (for openmpi)
>>>>>> if [ "$LD_LIBRARY_PATH" ] ; then
>>>>>>  export LD_LIBRARY_PATH="$LD_LIBRARY_PATH'/usr/local/lib"
>>>>>> else
>>>>>>  export LD_LIBRARY_PATH="/usr/local/lib"
>>>>>> fi
>>>>>>
>>>>> Is this on your desktop or on the "parallel computer"?
>>>>
>>>>
>>>> On both "parallel computers" (there is my desktop, ssh to two uma-type
>>>> dual-opteron "parallel computers". Only one was active when the "test"
>>>> problems arose. While the (ten years old) destop is i386, both other
>>>> machines are amd64, i.e., all debian lenny. I prepare the input files
>>>> on the i386 and use it also as storage for backups.
>>>
>>> So, you only use your i386 desktop to ssh to the AMD64 machine,
>>> and to prepare input files, etc, right?
>>> The OpenMPI installation, the compilations you do, and the job runs
>>> all happen in the AMD64 system, right?
>>>
>>> BTW, do you use each of these systems separately on your
>>> MPI program runs,
>>> or do you use them together?
>>> If you use them together, are they connected through a network,
>>> and did you setup passowrdless ssh connections between them?
>>>
>>>> The "parallel
>>>> computer" has only the X server and a minimal window for a
>>>> two-dimensional graphics of amber.
>>>
>>> I don't know how amber works, so please tell me.
>>> Do you somehow interact with amber while it is running in parallel mode,
>>> using this "minimal window for a two dimensional graphics"?
>>> Or is this only a data post-processing activity that happens after the
>>> parallel run of amber finishes?
>>>
>>>> The other parallel computer has a
>>>> GeForce 6600 card with GLSL support, which I use to elaborate
>>>> graphically the outputs from the numerical computations (using VMD,
>>>> Chimera and other 64 bit graphical programs).
>>>>
>>>>
>>>>>> There is also
>>>>>>
>>>>>> MPICH_HOME=/usr/local
>>>>>> export MPICH_HOME
>>>>>>
>>>>>> this is for DOCK, which, with this env variabl, accepts openmpi (at
>>>>>> lest it was so with v 1.2.6)
>>>>>>
>>>>> Oh, well, it looks like there is MPICH already installed on /usr/local.
>>>>> So, this may be part of the confusion, the path confusion I referred to.
>>>>
>>>> No, there is no MPICH installed. With the above export, DOCK (a
>>>> docking program from the same developers of Amber) is so kind to use
>>>> the executables of openmpi. The export was suggested by the DOCK
>>>> developers, and it worked. Unable to explain why.
>>>>
>>>
>>> OK, this may be a way the DOCK developers found to trick their own
>>> software (DOCK) to think MPICH is installed in /usr/local,
>>> and actually use the OpenMPI libraries instead of MPICH.
>>> They may have hardwired on their build scripts the "MPICH_HOME"
>>> environment variable as the location where the MPI libraries reside.
>>> But which MPI libraries are there may not matter much, I would guess.
>>> Just a guess anyway.
>>> (I have no idea of what the heck DOCK is or how it works.)
>>>
>>>> As far as the parallel support is concerned, /usr/local/bin only
>>>> contains what openmpi 1.3.1 has installed (resulting from ./configure
>>>> cc=/path/icc cxx=/path/icpc F77=path/ifort FC=path/ifort
>>>> --with-libnuma=/usr/lib):
>>>> mpic++ mpicc mpiCC mpicc-vt mpiCC-vt mpic++-vt mpicxx mpicxx-vt
>>>> mpiexec mpif77 mpif77-vt mpif90 mpif90-vt mpirun ompi-clean ompi-info
>>>> ompi-ps ompi-server opal-wapper opari orte-clean orted orte-iof
>>>> orte-ps orterun otfaux otfcompress otfconfig otfdecompress otfdump
>>>> otfmerge vtcc vtcxx vtf77 vtf90 vtfilter vtunify. There is no
>>>> orte_info.
>>>>
>>>
>>> Of course not.
>>> Doh!  I misspelled the name ... :(
>>> It is ompi_info for sure.
>>>
>>>>
>>>>> I would suggest installing OpenMPI on a different directory,
>>>>> using the --prefix option of the OpenMPI configure script.
>>>>> Do configure --help for details about all configuration options.
>>>>>
>>>>>
>>>>>> the intel compilers (compiled ifort and icc, are sourced in both my
>>>>>> .bashrc and root home .bashrc.
>>>>>>
>>>>>> Thanks and apologies for my low level in these affairs. It is the
>>>>>> first time I am faced by such problems, with amd64, same intel
>>>>>> compilers, and openmpi 1.2.6 everything was in order.
>>>>>>
>>>>> To me it doesn't look like the problem is related to the new version
>>>>> of OpenMPI.
>>>>
>>>> I asked about that because I am using the same commands, .bashrc, etc
>>>> that worked with version 1.2.6. The computers are the same, the only
>>>> (non minor) difference is upgrading from amd64 etch to amd64 lenny (or
>>>> I am doing mistakes that I have not yet detected).
>>>
>>> Yes, but I still don't think it is some problem in OpenMPI 1.3.1 that is
>>> causing trouble here.
>>> If it were, the program would start running, but mpirun is having trouble
>>> even to start the programs, right?
>>>
>>> Since you seem to have also upgraded the Debian release,
>>> therefore another part of the system also changed.
>>> But still, it may not be related to Debian either.
>>> It may be just some confusion on paths, etc.
>>>
>>> I really encourage you to try to compile and run the programs in the
>>> examples directory.
>>> They are very clear and simple (as opposed to amber, which hides behind
>>> a few layers of software), and even if they fail, the failure will help
>>> clarify the nature of the problem, and find a fix.
>>>
>>> Oh, well, I am afraid I am asking more questions than helping out,
>>> but I am trying to understand what is going on.
>>>
>>> Gus Correa
>>>
>>>>> Try the test programs with full path names first.
>>>>> It may not solve the problem, but it may clarify things a bit.
>>>>>
>>>>> Gus Correa
>>>>> ---------------------------------------------------------------------
>>>>> Gustavo Correa
>>>>> Lamont-Doherty Earth Observatory - Columbia University
>>>>> Palisades, NY, 10964-8000 - USA
>>>>> ---------------------------------------------------------------------
>>>>>
>>>>>> francesco
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Do "/full/path/to/openmpi/bin/mpirun --help" for details.
>>>>>>>
>>>>>>> I am not familiar to amber, but how does it find your openmpi
>>>>>>> libraries and compiler wrappers?
>>>>>>> Don't you need to give it the paths during configuration,
>>>>>>> say,
>>>>>>> /configure_amber -openmpi=/full/path/to/openmpi
>>>>>>> or similar?
>>>>>>>
>>>>>>> I hope this helps.
>>>>>>> Gus Correa
>>>>>>> ---------------------------------------------------------------------
>>>>>>> Gustavo Correa
>>>>>>> Lamont-Doherty Earth Observatory - Columbia University
>>>>>>> Palisades, NY, 10964-8000 - USA
>>>>>>> ---------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> Francesco Pietra wrote:
>>>>>>>>
>>>>>>>> I have compiled openmpi 1.3.1 on debian amd64 lenny with icc/ifort
>>>>>>>> (10.1.015) and libnuma. Tests passed:
>>>>>>>>
>>>>>>>> ompi_info | grep libnuma
>>>>>>>>  MCA affinity: libnuma (MCA v 2.0, API 2.0)
>>>>>>>>
>>>>>>>> ompi_info | grep maffinity
>>>>>>>>  MCA affinity: first use (MCA as above)
>>>>>>>>  MCA affinity: libnuma as above.
>>>>>>>>
>>>>>>>> Then, I have compiled parallel a molecular dynamics package, amber10,
>>>>>>>> without error signals but I am having problems in testing the amber
>>>>>>>> parallel installation.
>>>>>>>>
>>>>>>>> amber10 configure was set as:
>>>>>>>>
>>>>>>>> ./configure_amber -openmpi -nobintray ifort
>>>>>>>>
>>>>>>>> just as I used before with openmpi 1.2.6. Could you say if the
>>>>>>>> -openmpi should be changed?
>>>>>>>>
>>>>>>>> cd tests
>>>>>>>>
>>>>>>>> export DO_PARALLEL='mpirun -np 4'
>>>>>>>>
>>>>>>>> make test.parallel.MM  < /dev/null
>>>>>>>>
>>>>>>>> cd cytosine && ./Run.cytosine
>>>>>>>> The authenticity of host deb64 (which is the hostname) (127.0.1.1)
>>>>>>>> can't be established.
>>>>>>>> RSA fingerprint .....
>>>>>>>> connecting ?
>>>>>>>>
>>>>>>>> I stopped the ssh daemon, whereby tests were interrupted because deb64
>>>>>>>> (i.e., itself) could no more be accessed. Further attempts under these
>>>>>>>> conditions failed for the same reason. Now, sshing to deb64 is no more
>>>>>>>> possible: port 22 closed. In contrast, sshing from deb64 to other
>>>>>>>> computers occurs passwordless. No such problems arose at the time of
>>>>>>>> amd64 etch with the same
>>>>>>>> configuration of ssh, same compilers, and openmpi 1.2.6.
>>>>>>>>
>>>>>>>> I am here because the warning from the amber site is that I should to
>>>>>>>> learn how to use my installation of MPI. Therefore, if there is any
>>>>>>>> clue ..
>>>>>>>>
>>>>>>>> thanks
>>>>>>>> francesco pietra
>>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>> _______________________________________________
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>>>>>
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>>>>
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