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Re^9: Firefly-8.0.1 is not running on system with Intel MPI-4.1.X...

Siddheshwar Chopra

Dear Sir,
I followed the steps suggested by you regarding running the i/p file using qff2. Sir, I ran the job, and got the two files with extensions ".e" and ".o". Please find attached the ".e" file. I could not get any output file after running qff2 inputfile.inp. Please have a look at the file attached and let me know what is happening. As I understand it, it failed to create .out file.. Should I make it .log? Please elaborate the .e file Sir.

Could you confirm that it finally read the input file?? Let me know.


On Thu Mar 20 '14 6:24pm, Pavlo Solntsev wrote
>You don't need to run ~/.firefly.conf file. It is a configuration file but not a script.

>delete ~/.firelfy.conf (just in case) or use -s argument for qff2 (see qff2 --help)

>1) run "qff2 basename.inp". Where basename.inp is your input file.
>At this step, ~/.firefly.conf script will be created. Also, you will see file or basename.pbs in your current folder. They are scripts. Only one file will be generated or basename.pbs.
>2) run firelfy by typing "bash" or "qsub basename.pbs"

>Next time just type qff2 inputfile. Since you already have ~/.firefly.conf script will not ask you for information to create it again. If you want to change some default parameters you don't need to regenerate ~/.firelfy.conf. Instead, you can edit ~/,firelfy.conf manually.
>see qff2 --help for more options.

>On Thu Mar 20 '14 3:04pm, Siddheshwar Chopra wrote
>>Dear Pavel Sir,
>>I am thankful to you for providing the qff2 script. I have successfully generated a "firefly.conf" file. But what should I do next? I am running "qff2 firefly.conf" now, but it is again and again asking me the details which were already provided to create firefly.conf. What I have to do next Sir?

>>On Wed Mar 19 '14 6:54pm, Pavlo Solntsev wrote
>>>Dear Siddheshwar.

>>>I attached a script to configure FF. It will create a configuration file in your home folder ~/.firefly.conf with all default configurations.

>>>Place the script into a folder which is in PATH variable and make sure it is executable.
>>>Start using the script by typing

>>>qff2 inputfile

>>>If ~/.firefly.conf is not available script will create it by asking common questions. Before you start make sure you now MPI home directory. The directory with bin and lib directories (32-bit). NBO license information,f if you have it. If you want to use more then one CPU make sure appropriate MPI libraries is installed together with mpirun/mpiexec. In your case IntelMPI.

>>>Depends on your answer, you will get file .sh or .pbs. First is suitable for submission without PBS, while second is suitable for PBS.

>>>You can overwrite default parameters by providing appropriate parameters to the script. See qff2 --help.

>>>Also, you can create new parameters in ~/.firefly.conf by executing qff2 -s or change parameters manually in ~/.firefly.conf by using any text editor.

>>>Also, make sure you have Firefly linked with IntelMPI(!).

>>>Let me know if you have any problem.

>>>On Wed Mar 19 '14 12:28pm, Siddheshwar Chopra wrote
>>>>Dear Pavel Sir,
>>>>Thanks for encouraging me to go elaborately trough the manual. The points I noted from it:

>>>>1) I need to provide paths to bin and lib folders.. both for 32 bit Intel MPI..

>>>>2) There is a mention of Intel MPI-v3.x in the manual..

>>>>The Problem::

>>>>So I checked on my system and found that it has ONLY Intel MPI- v4.1.x (32 and 64 bit both) installed... SO I added the paths to 32-bit bin and lib folders.. which were inside ..../impi/
>>>>Did I do right?? But the problem persists giving error "Unable to open input file".. File permissions are also proper.

>>>>Please help.

>>>>On Tue Mar 18 '14 6:35pm, Pavlo Solntsev wrote
>>>>>Short answer - no.
>>>>>In any case you need a 32-bit library available via $LD_LIBRARY_PATH.

>>>>>Please, read "Linux MPI implementations" section from the manual.
>>>>>Check also "Installing Firefly on an InfiniBand network 64-bit Linux cluster
>>>>>with Intel MPI v. 3.x". You can skip configuration InfiniBand and go directly to IntelMPI setup.

>>>>>Again, read very carefully the manual and use a search. There is also manual - how to setup FF with OpenMPI. Please, search on this forum.

>>>>>On Tue Mar 18 '14 12:37pm, Siddheshwar Chopra wrote
>>>>>>Dear Sir,
>>>>>>Please note the configuration of the system on which I have copied the FIREFLY-8.0.1 folder (for Intel MPI version)::
>>>>>>64 Bit Cent OS, and with Intel MPI-4.0.X
>>>>>>Are there Statically linked versions available for Intel MPI ones?

>>>>>>Please help me.

>>>>>>On Sun Mar 16 '14 6:01am, Pavlo Solntsev wrote
>>>>>>>Dear Siddheshwar.

>>>>>>>Please, use the search tool-chain for this site. All you problems were discussed in this forum.
>>>>>>>1) Read the manual, specifically command line section (how to run FF)
>>>>>>>2) Manual also has example of script how to run FF exactly with IntelMPI. do search.
>>>>>>>3) If you can't find answer by using search and/or manual, put EXACT command line or script you use to tun FF.

>>>>>>>If you need a help with scripting i may help.

>>>>>>>On Sat Mar 15 '14 9:32am, Siddheshwar Chopra wrote
>>>>>>>>Dear Sir,
>>>>>>>>I could manage to remove the  "Unable to open input file" error by giving the absolute path to the i/p file.. But now I am struggling with the following persistent error::

>>>>>>>>p4_error: semget failed for setnum: 0

>>>>>>>>Over the internet I came across "cleanipcs". Please help me..I am unable to progress with my work. This error is repeating everytime; not allowing the program to run.


>>>>>>>>On Sat Mar 15 '14 7:27am, Siddheshwar Chopra wrote
>>>>>>>>>Dear Sir,
>>>>>>>>>Yes I have read the manual.. Could you please point out the mistake Sir. Perhaps it is a very silly mistake. I am new to Linux and need to stay with it for a while. Please help.


>>>>>>>>>On Fri Mar 14 '14 10:06pm, Pavlo Solntsev wrote
>>>>>>>>>>Dear Siddheshwar.

>>>>>>>>>>Did you consult the manual for Firefly's command line options?

>>>>>>>>>>On Fri Mar 14 '14 3:06pm, Siddheshwar Chopra wrote
>>>>>>>>>>>Dear Sir,
>>>>>>>>>>>I am running Firefly801 executable file from unzipped ff801 (relatively located) folder. The system has Intel MPI installed on it. I am running an i/p file xyz.inp located inside ff801/INPUT directory using ::

>>>>>>>>>>>mpirun -np 2 ./firefly801 -r -f -p -i /path/INPUT/xyz.inp
>>>>>>>>>>>But I am getting this error:::


>>>>>>>>>>> ON MASTER NODE, ERROR CODE IS : 0x00000001
>>>>>>>>>>>    Unable to open input file

>>>>>>>>>>>Also please tell how to use -stdext -ex?? What is it used for??


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