PLSAMA installation problems

Open forum for general discussions relating to PLASMA.

PLSAMA installation problems

Postby ElenaB » Tue Feb 19, 2013 9:24 am

Hello,

I installed the PLASMA library 2.5.0 on a Cray XE6 (via the python script).
I am planning to use PLASMA with Fortran code. The operating system is CLE: 4.0.UP03. I ran:

./setup.py --prefix=$HOME --blaslib="L$CRAY_LIBSCI_PREFIX_DIR/lib -lsci_cray_mp" --downblas --downlapc -cc cc --fc ftn



Basically all tests are passed. There are two lines from the installation output which don't look good, though:

sh: line 1: 21744 Segmentation fault (core dumped) xlintstc <
ctest.in

sh: line 1: 21747 Segmentation fault xlintstz < ztest.in


It produced a core, on which I used gdb:

gdb ./xlintstc core
...
Program terminated with signal 11, Segmentation fault.

#0 0x00000000009cc08d in
tcmalloc::CentralFreeList::RemoveRange(void**,
void**, int) ()

I assume tcmalloc comes through the cblas lib I had to download for PLASMA.


I also used 'bt' with the core:


#0 0x00000000009cc08d in tcmalloc::CentralFreeList::RemoveRange(void**, void**, int) ()
#1 0x00000000009d04fb in tcmalloc::ThreadCache::FetchFromCentralCache(unsigned long, unsigned long) ()
#2 0x00000000009c5f1a in (anonymous namespace)::do_memalign(unsigned long, unsigned long) ()
#3 0x0000000000a494f1 in tc_posix_memalign ()
warning: Range for type (null) has invalid bounds 0..-121
...
#4 0x00000000005c639c in quark_malloc$$CFE_id_72c6b376_808455b3 (size=<optimized out>) at quark.c:415
#5 0x00000000005c8775 in quark_check_and_queue_ready_task$$CFE_id_72c6b376_808455b3 (quark=<optimized out>,
task=<optimized out>, worker_rank=<optimized out>) at quark.c:1511
#6 0x00000000005c9d92 in quark_address_set_node_initial_check_and_launch$$CFE_id_72c6b376_808455b3 (
quark=<optimized out>, address_set_node=<optimized out>, completed_dep=<optimized out>, worker_rank=<optimized out>)
at quark.c:2375
#7 0x00000000005ca063 in quark_remove_completed_task_and_check_for_ready$$CFE_id_72c6b376_808455b3 (
quark=<optimized out>, task=<optimized out>, worker_rank=<optimized out>) at quark.c:2454
#8 0x00000000005c9ba8 in quark_process_completed_tasks$$CFE_id_72c6b376_808455b3 (quark=<optimized out>)
at quark.c:2328
#9 0x00000000005c758a in QUARK_Barrier (quark=<optimized out>) at quark.c:916
#10 0x00000000005c76ae in QUARK_Waitall (quark=<optimized out>) at quark.c:959
#11 0x00000000004eed09 in PLASMA_cungqr (M=<optimized out>, N=<optimized out>, K=<optimized out>, A=<optimized out>,
LDA=<optimized out>, descT=<optimized out>, Q=<optimized out>, LDQ=<optimized out>) at cungqr.c:138
#12 0x00000000004b308b in plasma_cungqr_ (M=<optimized out>, N=<optimized out>, K=<optimized out>, A=<optimized out>,
LDA=<optimized out>, descT=<optimized out>, B=<optimized out>, LDB=<optimized out>, info=<optimized out>)
at plasma_cf77.c:434
#13 0x000000000046c3b0 in cqrt03 (m=<optimized out>, n=<optimized out>, k=<optimized out>, af=<optimized out>,
c=<optimized out>, cc=<optimized out>, q=<optimized out>, lda=<optimized out>, t=<optimized out>,
work=<optimized out>, lwork=<optimized out>, rwork=<optimized out>, result=<optimized out>) at cqrt03.f:130
#14 0x0000000000467c38 in cchkqr (dotype=<optimized out>, nm=<optimized out>, mval=<optimized out>, nn=<optimized out>,
nval=<optimized out>, nnb=<optimized out>, nbval=<optimized out>, nxval=<optimized out>, ibval=<optimized out>,
nrhs=<optimized out>, thresh=<optimized out>, tsterr=<optimized out>, nmax=<optimized out>, a=<optimized out>,
af=<optimized out>, aq=<optimized out>, ar=<optimized out>, ac=<optimized out>, b=<optimized out>,
x=<optimized out>, xact=<optimized out>, tau=<optimized out>, work=<optimized out>, rwork=<optimized out>,
iwork=<optimized out>, nout=<optimized out>) at cchkqr.f:299
warning: Range for type (null) has invalid bounds 1..-72
warning: Range for type (null) has invalid bounds 1..-72
warning: Range for type (null) has invalid bounds 1..-72
warning: Range for type (null) has invalid bounds 1..-72
warning: Range for type (null) has invalid bounds 1..-128
warning: Range for type (null) has invalid bounds 1..-128
warning: Range for type (null) has invalid bounds 1..-128
warning: Range for type (null) has invalid bounds 1..-128
warning: Range for type (null) has invalid bounds 1..-88
warning: Range for type (null) has invalid bounds 1..-112
warning: Range for type (null) has invalid bounds 1..-48
warning: Range for type (null) has invalid bounds 1..-24
warning: Range for type (null) has invalid bounds 1..-24
warning: Range for type (null) has invalid bounds 1..-126
#15 0x0000000000447ae7 in CCHKAA () at cchkaa.f:513
#16 0x00000000009e1114 in __libc_start_main (main=0x443ce0 <CCHKAA>, argc=1, ubp_av=0x7fffffffb298, init=0,
fini=0x7fffffffada0, rtld_fini=0x7fffffffada0, stack_end=0x7fffffffb288) at libc-start.c:226
#17 0x0000000000408091 in _start () at ../sysdeps/x86_64/elf/start.S:113

Thanks in advance,
Elena
ElenaB
 
Posts: 3
Joined: Tue Feb 05, 2013 5:29 am

Re: PLSAMA installation problems

Postby admin » Tue Feb 19, 2013 9:44 am

Elena,
Sorry for the late reply.
Please take a look at this:

https://bluewaters.ncsa.illinois.edu/known-issues
"TCMALLOC: Codes may crash in tcmalloc. Cray is working on fixing these. In the mean time, use the flag "-hsystem_alloc" to avoid linking in tcmalloc. Using this flag may result in a new set of problems. So use it with caution. Continue to open bugs on Jira if you see problems with tcmalloc."

Please let us know if it fixes the problem.
Best,
Jakub
admin
Site Admin
 
Posts: 79
Joined: Wed May 13, 2009 1:27 pm

Re: PLSAMA installation problems

Postby ElenaB » Thu Mar 14, 2013 8:48 am

Hello,

It did fix the problem! Many thanks,

Elena
ElenaB
 
Posts: 3
Joined: Tue Feb 05, 2013 5:29 am

Re: PLSAMA installation problems

Postby jyoti pandey » Mon Apr 15, 2013 3:05 am

hii all...i'm also having a problem in installing plasma...while running ./setup.py command following error is coming...

jpandey@jyoti:~/Downloads/plasma-installer_2.5.0b1$ ./setup.py
Traceback (most recent call last):
File "./setup.py", line 70, in <module>
sys.exit(main(sys.argv))
File "./setup.py", line 40, in main
fp = open("history.log",'a')
IOError: [Errno 13] Permission denied: 'history.log'

plz tell me how to resolve ds problem...
and what are the steps to install plasma_2.5.0 completely on ubuntu 12.04 (i686 machine)

thank u...
jyoti pandey
 
Posts: 5
Joined: Mon Apr 15, 2013 2:38 am

Re: PLSAMA installation problems

Postby admin » Mon Apr 15, 2013 8:32 am

Looks like the script cannot create the history.log file.
Seems to be a problem with permissions.
Make sure the script can write the files.
Jakub
admin
Site Admin
 
Posts: 79
Joined: Wed May 13, 2009 1:27 pm

Re: PLSAMA installation problems

Postby jyoti pandey » Tue Apr 16, 2013 1:44 am

hello ..
i,m unable to install plasma using plasma installer..plz help me.
when i'm typing
./setup.py --cc gcc --fc gfortran --downblas
it's giving following error

BLAS installation/verification
========================================

The reference BLAS library is being installed.
Don't expect high performance from this reference library!
If you want performance, you need to use an optimized BLAS library and,
to avoid unnecessary complications, if you need to compile this optimized BLAS
library, use the same compiler you're using here.
Downloading reference BLAS...
=================================================================================
Cannot download./blas.tgz
Make sure the network is reachable.
Packages may be downloaded with wget though a proxy; in order to
enable this feature it is enough the set the http_proxy environment
variable (read the wget man pages for more details).
If you still have troubles, you can manually download ./blas.tgz from this URL:
http://netlib.org/blas/blas.tgz
into the current directory:
/home/jyoti/Downloads/plasma-installer_2.5.0b1/build/download
Traceback (most recent call last):
File "./setup.py", line 70, in <module>
sys.exit(main(sys.argv))
File "./setup.py", line 50, in main
Blas(config, plasma)
File "/home/jyoti/Downloads/plasma-installer_2.5.0b1/script/blas.py", line 41, in __init__
self.down_install_blas()
File "/home/jyoti/Downloads/plasma-installer_2.5.0b1/script/blas.py", line 127, in down_install_blas
downloader(self.blasurl,self.downcmd)
File "/home/jyoti/Downloads/plasma-installer_2.5.0b1/script/utils.py", line 153, in downloader
shutil.copy('download/'+name, './')
File "/usr/lib/python2.7/shutil.py", line 119, in copy
copyfile(src, dst)
File "/usr/lib/python2.7/shutil.py", line 82, in copyfile
with open(src, 'rb') as fsrc:
IOError: [Errno 2] No such file or directory: 'download/./blas.tgz'
jyoti@jyoti-Compaq-Presario-CQ45-NoteBook-PC:~/Downloads/plasma-installer_2.5.0b1$

what to do in order to get rid of dis problem...and plz tell m i following right installation procedure if not then plzz tell me right steps for it's installation....

thanking u....
jyoti pandey
 
Posts: 5
Joined: Mon Apr 15, 2013 2:38 am

Re: PLSAMA installation problems

Postby jyoti pandey » Tue Apr 16, 2013 1:48 am

i downloaded blas.tgz into specified directory bt still getting the same error.... :(
jyoti pandey
 
Posts: 5
Joined: Mon Apr 15, 2013 2:38 am

Re: PLSAMA installation problems

Postby jyoti pandey » Tue Apr 16, 2013 12:43 pm

somebody plz reply...it's really urgent..
jyoti pandey
 
Posts: 5
Joined: Mon Apr 15, 2013 2:38 am


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