GCHP Timing Tests

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GCHP Home

Overview

This page features reports of user run-times done with High Performance GEOS-Chem (GCHP). If you are running GCHP please add your own results below. You can sign up for a wiki account to edit this page or you can send your information to the GEOS-Chem Support Team.

Extracting GCHP Timing Information

Follow instructions on Getting Started with GCHP to get set up to run GCHP. GCHP timing information is displayed at the end of the GCHP.log log file. Please report the numbers for items in red below.

Total time for GEOS-Chem core components, in seconds:

 Times for GIGCchem
TOTAL                   :   16195.289
INITIALIZE              :      64.237 
RUN                     :   16010.216
FINALIZE                :       0.000
DO_CHEM                 :   15682.849
CP_BFRE                 :       7.515
CP_AFTR                 :     172.251
GC_CONV                 :    1062.171
GC_EMIS                 :     846.439
GC_DRYDEP               :       5.876
GC_FLUXES               :       0.000
GC_TURB                 :     802.816
GC_CHEM                 :   12009.869
GC_WETDEP               :     729.897
GC_DIAGN                :       0.000
GenInitTot              :      49.299
--GenInitMine           :      49.299
GenRunTot               :       0.000
--GenRunMine            :       0.000 
GenFinalTot             :      35.596
--GenFinalMine          :      35.596
GenRecordTot            :      25.848
--GenRecordMine         :      25.845
GenRefreshTot           :       0.000
--GenRefreshMine        :       0.000

Total run-time, in seconds:

  -----------------------------------------------------
     Block          User time  System Time   Total Time
  -----------------------------------------------------
  TOTAL                    34848.6779       0.0000   34848.6779
  COMM_TOTAL                 552.8329       0.0000     552.8329
  COMM_TRAC                  552.8318       0.0000     552.8318
  FV_TP_2D                  6004.5731       0.0000    6004.5731

Total time for advection, in seconds:

 Times for DYNAMICS
TOTAL                   :    7645.593
INITIALIZE              :       1.029
RUN                     :    7645.563
FINALIZE                :       0.000
GenInitTot              :       0.012
--GenInitMine           :       0.012
GenRunTot               :       0.000
--GenRunMine            :       0.000
GenFinalTot             :       0.000
--GenFinalMine          :       0.000
GenRecordTot            :       0.008
--GenRecordMine         :       0.006
GenRefreshTot           :       0.000
--GenRefreshMine        :       0.000

Total time for MAPL History, in seconds:

 Times for HIST
TOTAL                   :     211.554
Initialize              :       4.994
Finalize                :       0.142
Run                     :     206.592
--Couplers              :      54.423
--I/O                   :     152.310
----IO Create           :       1.789
----IO Write            :     152.310
-----IO Post            :       5.638
-----IO Wait            :      40.447
-----IO Write           :     110.306
-ParserRun              :       0.000
GenInitTot              :       0.000
--GenInitMine           :       0.000
GenRunTot               :       0.000
--GenRunMine            :       0.000
GenFinalTot             :       0.002
--GenFinalMine          :       0.002
GenRecordTot            :       0.000
--GenRecordMine         :       0.000
GenRefreshTot           :       0.000
--GenRefreshMine        :       0.000
  

Total time for MAPL ExtData, in seconds:

 Times for EXTDATA
TOTAL                   :    2840.095
Initialize              :       8.410
Run                     :    2831.698
-Read_Loop              :    2800.662
--CheckUpd              :       6.597
--Read                  :    2702.010
--Swap                  :       1.650
--Bracket               :      99.195
-Interpolate            :      31.540
GenInitTot              :       0.007
--GenInitMine           :       0.006
GenRunTot               :       0.005
--GenRunMine            :       0.003
GenFinalTot             :       0.006
--GenFinalMine          :       0.006
GenRecordTot            :       0.000
--GenRecordMine         :       0.000
GenRefreshTot           :       0.000
--GenRefreshMine        :       0.000

Reported Model Runs

If you are running GCHP we encourage you to report performance in this section. For optimal comparability we recommend doing a 7-day duration simulation but information for other durations is welcome as well. Run settings may vary considerably but we ask that the following be constant:

  • Jobs start on model date 2016/07/01 00:00 GMT.
  • The code was compiled from the standard GCHP run directory (gchp_standard) with the option make compile_clean.

Enter your system information in the top table to the best of your knowledge and your simulation information in the bottom table. Use a unique id to cross-reference between the two.

Enter your system information here:

ID Organization Cluster Partition OS Network interconnect CPU Vendor CPU Model CPU Speed [MHz] Compiler MPI NetCDF Filesystem info
000 Harvard Odyssey huce_intel CentOS 7 Infiniband Intel Xeon 2.10GHz intel 17.0.4 openmpi 3.1.1 netcdf 4.1.3 LFS
001 Harvard Odyssey huce_intel CentOS 7 Infiniband Intel Xeon 2.10GHz gcc 7.1.0 openmpi 3.1.1 netcdf 4.1.3 LFS
002 Harvard Odyssey huce_intel CentOS 7 Infiniband Intel Xeon 2.10GHz gcc 8.2.0 openmpi 3.1.1 netcdf 4.1.3 LFS
003 Harvard Odyssey huce_amd CentOS 7 Infiniband AMD Opteron 2.3GHz gcc 8.2.0 openmpi 3.1.1 netcdf 4.1.3 LFS


If you needed to change GCHP source code or make customized environment variables for a successful compilation and run on your system, please list the necessary changes here:

ID OS Compiler MPI Source Code Changes Special Env Variables


Enter your simulation information here:

User ID GEOS-Chem Version Total Nodes Total Cores Simulation Duration Met Source Met Res Grid Res Dyn dt [min] Chem dt [min] Diagnostics* Diag Freq Diag Duration Total Time
(s)
Dynamics
(s)
GIGCchem
(s)
History
(s)
ExtData
(s)


Bob Yantosca 001 12.0.1 1 6 standard 6 hours GEOS-FP 0.25x0.3125 c24 10 20 default 1hr 1hr 1080
(18.0 min)
83 412 145 427
Bob Yantosca 002 12.0.1 1 6 standard 6 hours GEOS-FP 0.25x0.3125 c24 10 20 default 1hr 1hr 967
(16.1 min)
73 351 125 406
Lizzie Lundgren 000 12.0.1 3 48 standard 7 days GEOS-FP 0.25x0.3125 c90 10 20 default daily daily 31644
(8.78 hrs)
4753 16279 177 2961
Lizzie Lundgren 001 12.0.1 3 48 standard 7 days GEOS-FP 0.25x0.3125 c90 10 20 default daily daily 34848
(9.67 hrs)
7645 16195 211 2840
Lizzie Lundgren 002 12.0.1 3 48 standard 7 days GEOS-FP 0.25x0.3125 c90 10 20 default daily daily 37283
(10.35 hrs)
7345 17742 323 3140
Bob Yantosca 003 12.0.1 1 6 standard 1 hour GEOS-FP 0.25x0.3125 c24 10 20 default hourly hourly 1015
(17 min)
28 269 47 693
Bob Yantosca 002 12.0.1 1 6 standard 1 hour GEOS-FP 0.25x0.3125 c24 10 20 default hourly hourly 525
(9 min)
13 110 19 403

*Default diagnostics include the SpeciesConc and StateMet collections only.

Graphs of Model Run Times

These will be generated when we have a critical mass of data.

Archive of Previously Submitted Reports

Submission from Colin Lee, Dalhousie University:

Cluster name Compilers MPI NetCDF library # of Nodes # of CPUs GCHP version Grid resolution Duration [days-hrs] Met source Met resolution Dynamic timestep [min] Chemistry timestep [min] Total run time [hrs]
Graham ifort 2016 openmpi 2.1.1 4 1 24 ??? c24 31-0 GEOS-FP 2x25 10 20 14:22
Graham ifort 2016 openmpi 2.1.1 4 4 96 ??? c96 0-1 GEOS-FP 2x25 5 20 0:18
Graham ifort 2016 openmpi 2.1.1 4 4 96 ??? c96 0-1 GEOS-FP 0.25x0.3125 5 20 0:30
Graham ifort 2016 openmpi 2.1.1 4 72 864 ??? c360 0-1 GEOS-FP 2x2.5 5 20 1:30
Graham ifort 2016 openmpi 2.1.1 4 72 864 ??? c360 1-0 GEOS-FP 2x2.5 5 20 6:57
  • Running on > approx. 1000 cores at c360 appears to cause a seg fault in call to SIN function around CubeToLaLon.F90:432

Submission from Sebastian Eastham, MIT (LAE)

Cluster name Compilers MPI NetCDF library # of Nodes # or CPUs GCHP version Grid resolution Duration [days-hrs] Met source Met resolution Dynamic timestep [min] Chemistry timestep [min] Total run time [hrs]
Nehalem ifort 2015 MPICH2 v3.3 NetCDF C 4.4.1, NetCDF Fortran 4.4.4 2 36 11-02c C90 31-0 GEOS-FP 0.25x0.3125 5 10 68

Notes: using 36 cores out of a total of 48 available from 2 nodes with a 10 GB direct ethernet connection.