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

Pavlo Solntsev
pavlo.solntsev@gmail.com


Dear Siddheshwar.

Could you please give EXACT command you used to start FF. Step-by-step. How you created running script and how you executed it. Also, i would be glad to see the script too. Make sure all private information is removed from the script.

From the error file you sent, i found mistake in you path to the input and output files.

+ /usr/bin/time mpirun -np 1 /home/schopra/ff801intel/firefly801 -ex /home/schopra/ff801intel -i /home/schopra//home/schopra/ff801intel/INPUT/Si26H26.inp -o /home/schopra//home/schopra/ff801intel/INPUT/Si26H26.out -t /home/schopra/ff801intel/tmp/13216/

Once again, the script should be executed as :

qff2 inputfilename

Do not provide full path. For example, i have file H2.inp in some folder "dir1". I need:
$ cd dir1
$ qff2 h2.inp
$ bash h2.sh
or
$ qsub h2.pbs

Also, why do you use IntelMPI for one CPU? To debug IntelMPI, i would recommend you to use at least two CPUs.

Do you use PBS?

What exact file did you execute to get *.e and *.o files?

Please, answer all my questions. As soon as i get all this information it will be easy to go forward.

Sincerely,
Pavlo.



On Sat Mar 22 '14 10:53am, Siddheshwar Chopra wrote
---------------------------------------------------
>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.

>Regards,

>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 basename.sh or basename.pbs in your current folder. They are scripts. Only one file will be generated basename.sh or basename.pbs.
>>2) run firelfy by typing "bash basename.sh" 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.

>>Best,
>>Pavel.
>>
>>
>>
>>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?
>>>
>>>
>>>Regards,

>>>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.

>>>>Pavel.
>>>>
>>>>
>>>>
>>>>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/4.1.0.024/ia32/.
>>>>>Did I do right?? But the problem persists giving error "Unable to open input file".. File permissions are also proper.

>>>>>Please help.

>>>>>Regards,
>>>>>
>>>>>
>>>>>
>>>>>On Tue Mar 18 '14 6:35pm, Pavlo Solntsev wrote
>>>>>----------------------------------------------
>>>>>>Short answer - no.
>>>>>>In any case you need a 32-bit libmpi.so 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.

>>>>>>Pavel.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>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.

>>>>>>>>Pavlo.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>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.

>>>>>>>>>Regards,

>>>>>>>>>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.

>>>>>>>>>>Regards,

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

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

>>>>>>>>>>>Pavel.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>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:::

>>>>>>>>>>>>FATAL ERROR INITIALIZING FIREFLY! CHECK YOUR COMMAND LINE OPTIONS!

>>>>>>>>>>>> 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??

>>>>>>>>>>>>Regards,


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