thank you for your help. I think I found the reason:
... partitioning base files (geo, conlim, sections, zones and weirs)
+> /home/hafedh/v8p3r1/builds/debgfopenmpi/bin/partel < partel_T2DGEO.par >> partel_T2DGEO.log
... splitting / copying other input files
partitioning: T2ATMB
+> /home/hafedh/v8p3r1/builds/debgfopenmpi/bin/partel < partel_T2DGEO.par >> partel_T2ATMB.log
for the partition it uses the same file as input (partel_T2DGEO.par) for bith the GEO and Atmospheric files.
In fact, using python3 instead of python2.7, I got a problem with the the configuration file. PARTEL.PAR which is not created in the working directory. So I replaced it by partel_T2DGEO.par and this was working as far as I did not use input data in format file.
[debgfopenmpi]
#
#par_cmdexec: <config>/partel < PARTEL.PAR >> <partel.log>
par_cmdexec: <config>/partel < partel_T2DGEO.par >> <partel.log>