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NOTICE: This version of the NSF Unidata web site (archive.unidata.ucar.edu) is no longer being updated.
Current content can be found at unidata.ucar.edu.
To learn about what's going on, see About the Archive Site.
Hi I've run into a problem that is possibly a memory leak in the netCDF library (netcdf/4.3.0). When I use nf90_get_var to read from a series of netCDFarchives, memory leaks (andeventually uses up all RAM), even though every netCDF archive is closed before the next one is opened (chunk cache is not the cause). I attached ademonstration code (memory_leak_demo.tgz). It can be compiled by running the compile.sh script, after setting the FC (Fortran compiler) and NETCDF (path to netCDF library) environment variables. The demonstration code has two executables: memory_leak_demo_1: Creates one netCDF archivewith data, and reads the data from the archive once. memory_leak_demo_2 : Creates ten netCDF archives with data, and reads the data from each of the ten archives once. I attached PBS output logs for the two executables (compiled with intel/14.0.2): MEMORY_LEAK_DEMO_1_THEIA.sh.o5600419 MEMORY_LEAK_DEMO_2_THEIA.sh.o5600420 Comparing these, memory_leak_demo_2 uses about 5 times more memory than memory_leak_demo_1. I suspect this is a memory leak(unless I am missing something crucial). Jan
Attachment:
memory_leak_demo.tgz
Description: application/compressed-tar
Start Prologue v3.0-ad-2014.12.29 Mon Dec 7 21:01:39 UTC 2015 on Mother
Superior(head node): t1041
Node Access Status = SINGLEJOB
Job 5600419.bqs3 started for user Jan.Kazil in queue debug
======= Running Sanity Checks =======
----------------
t1041
----------------
PASS!
======= Ended Sanity Checks =======
End Prologue v3.0-ad-2014.12.29 Mon Dec 7 21:01:41 UTC 2015
_______________________________________________________________
Welcome to Theia
This system is Cray CS400 Linux Cluster
Update History:
Version: v3.0-ad-2014.12.29
-- Initial install on Cray systems
type:
module avail
for various Available Modules
_______________________________________________________
Writing netCDF archive test.nc
Done writing.
Reading netCDF archive test.nc
Done reading.
_______________________________________________________________
Start Epilogue v3.0-ad-2014.12.29 Mon Dec 7 21:01:43 UTC 2015
=====================================
Peak memory usage summary:
min = 572776 KB
ave = 572776 KB
max = 572776 KB
All nodes sorted by nodelist order: (memory usage in KB)
% of user user user total total
Node limit max limit current current phys
t1041 0.9 572776 63719424 291536 1738412 65997864
=====================================
Job 5600419.bqs3 finished for user Jan.Kazil in queue debug with exit code 0
Node Access Status = SINGLEJOB
Statistics cput=00:00:00,energy_used=0,mem=0kb,vmem=0kb,walltime=00:00:04
End Epilogue v3.0-ad-2014.12.29 Mon Dec 7 21:01:44 UTC 2015
_______________________________________________________________
Start Prologue v3.0-ad-2014.12.29 Mon Dec 7 21:01:39 UTC 2015 on Mother
Superior(head node): t1054
Node Access Status = SINGLEJOB
Job 5600420.bqs3 started for user Jan.Kazil in queue debug
======= Running Sanity Checks =======
----------------
t1054
----------------
PASS!
======= Ended Sanity Checks =======
End Prologue v3.0-ad-2014.12.29 Mon Dec 7 21:01:41 UTC 2015
_______________________________________________________________
Welcome to Theia
This system is Cray CS400 Linux Cluster
Update History:
Version: v3.0-ad-2014.12.29
-- Initial install on Cray systems
type:
module avail
for various Available Modules
_______________________________________________________
Writing netCDF archive test_0.nc
Writing netCDF archive test_1.nc
Writing netCDF archive test_2.nc
Writing netCDF archive test_3.nc
Writing netCDF archive test_4.nc
Writing netCDF archive test_5.nc
Writing netCDF archive test_6.nc
Writing netCDF archive test_7.nc
Writing netCDF archive test_8.nc
Writing netCDF archive test_9.nc
Done writing.
Reading netCDF archive test_0.nc
Reading netCDF archive test_1.nc
Reading netCDF archive test_2.nc
Reading netCDF archive test_3.nc
Reading netCDF archive test_4.nc
Reading netCDF archive test_5.nc
Reading netCDF archive test_6.nc
Reading netCDF archive test_7.nc
Reading netCDF archive test_8.nc
Reading netCDF archive test_9.nc
Done reading.
_______________________________________________________________
Start Epilogue v3.0-ad-2014.12.29 Mon Dec 7 21:01:56 UTC 2015
=====================================
Peak memory usage summary:
min = 3067060 KB
ave = 3067060 KB
max = 3067060 KB
All nodes sorted by nodelist order: (memory usage in KB)
% of user user user total total
Node limit max limit current current phys
t1054 4.8 3067060 63719424 2791012 4224968 65997864
=====================================
Job 5600420.bqs3 finished for user Jan.Kazil in queue debug with exit code 0
Node Access Status = SINGLEJOB
Statistics
cput=00:00:09,energy_used=0,mem=284804kb,vmem=561384kb,walltime=00:00:17
End Epilogue v3.0-ad-2014.12.29 Mon Dec 7 21:01:57 UTC 2015
_______________________________________________________________
begin:vcard fn:Jan Kazil, PhD n:Kazil, PhD;Jan org:National Oceanic and Atmospheric Administration (NOAA);Chemical Sciences Division adr:325 Broadway;;Earth System Research Laboratory, R/CSD2;Boulder;CO;80305;USA email;internet:jan.kazil@xxxxxxxx title:CIRES Scientist III tel;work:+1 303 497 5820 tel;fax:+1 303 497 5340 version:2.1 end:vcard
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