Hi Mike,
What compiler are you using? What ./configure command-line options did
you use? Did you run ./configure with --enable-MPI_Alloc_mem? I
personally develop and test on SuSE, rocks 3.3 (which is a RHEL
derivitive), windows, and occasionally OS X.
To further track this problem down it may be necessary to compile with
debug options and run the program with a debugger attached. If you can
send me the query data set (off the list) I can try to reproduce the
problem.
-Aaron
Mike Schilling wrote:
Unfortunately I send the mail partially already - but incomplete -
sorry for posting again ...
-------------
Hallo everybody,
... I try to run mpiblast on a 17 node (2proc each) oscar 4.2 cluster
based on RHEL 4. The master node is a dual Xeon2.4 while the 16
workers are dual Pentium III (933).
All cluster tests described in the oscar installation were successful
and also I was able to compile the NCBI toolbox (patch included)
without problems. Mpiblast was compiled using the following options:
--with-ncbi=/usr/local/ncbi and --with-mpi=/opt/lam-7.0.6
This was successful as well. Blasting very small contigs (8kb) against
the uniprot database works perfect and fast. When I try to go with
querys over 30kb in size the following error occur after roughly 5 min:
mpirun -np 34 /usr/local/bin/mpiblast
--debug=/database/tmpfiledir/debug -p blastx -d uniprot -i
/database/tmpfiledir/contig76_53738-84646.tmp -o
/database/results/contigs_masked.out
*** glibc detected *** free(): invalid pointer: 0x08a34870 ***
-----------------------------------------------------------------------------
One of the processes started by mpirun has exited with a nonzero exit
code. This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.
PID 20219 failed on node n7 (10.0.0.8) due to signal 6.
-----------------------------------------------------------------------------
2 134.052 Bailing out with signal -1
3 134.054 Bailing out with signal -1
4 134.055 Bailing out with signal -1
5 134.057 Bailing out with signal -1
67 134.059 Bailing out with signal -1
134.06 Bailing out with signal -1
89 134.063 Bailing out with signal -1
134.063 Bailing out with signal -1
1011 134.066 Bailing out with signal -1
134.066 Bailing out with signal -1
12 134.069 Bailing out with signal -1
15 134.071 Bailing out with signal -1
13 134.071 Bailing out with signal -1
17 134.076 Bailing out with signal -1
16 134.076 Bailing out with signal -1
18 134.077 Bailing out with signal -1
19 134.078 Bailing out with signal -1
20 134.08 Bailing out with signal -1
21 134.081 Bailing out with signal -1
22 23 134.084 Bailing out with signal -1
134.084 Bailing out with signal -124 134.086 Bailing out with
signal -1
25 134.088 Bailing out with signal
-1
27 134.09 Bailing out with signal -1
26 134.091 Bailing out with signal -1
28 134.09329 134.094 Bailing out with signal -1
Bailing out with signal -1
30 134.096 Bailing out with signal -1
32 134.099 Bailing out with signal -1
34 134.1 Bailing out with signal -1
33 134.101 Bailing out with signal -1
31 134.097 Bailing out with signal -1
35 134.1 Bailing out with signal -1
... there is no further bad message when I switch on debug logs - it
seems to break suddenly and the address of the "glibc free()" message
sometimes shows different numbers on different nodes ...
I tried the "-ssi rpi lamd" option of mpirun as well since there was
something in the manual in connection with lamd - same result ....
Next - I compiled both - the 2004 and the 2005 version of the ncbi
toolbox with a similar result. Also compiling against mpich or lam has
no influence. As well I tried to compile the 1.3.0 release of
mpiblast but without success.
Are there any things which I can do to get more debug output? Do you
have a recommendation about a kernel or a specific RHEL version (or
maybe a specific cluster software) where it runs since I do not
believe that it relies on hardware.
any help would be appreciated
best regards
Mike
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