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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