Run SUNDIALS on the Cluster¶
- SUNDIALS is a SUite of Nonlinear and DIfferential/ALgebraic equation Solvers.
- This guide will cover how to run SUNDIALS on the Cluster.
- This is a link to the SUNDIALS Homepage.
- SUNDIALS consists of 6 solvers that are targeted towards solving different problems
- When running SUNDIALS, you will choose the appropriate solver, vector type (serial or parallel), and language (C or FORTRAN).
- Then you will compile the program, specifying the appropriate libraries as flags and run it.
Walkthrough: Run SUNDIALS on the Cluster¶
- This walkthrough will work on a sample program that uses the CVODE linear solver interface in the solution of a 3-species chemical kinetics problem.
- More information about this example can be found in section 2.1 of the Example Programs for CVODE PDF provided by the Center for Applied Scientific Computing Lawrence Livermore National Laboratory.
- For more information about CVODE, please visit the User Documentation for CVODE.
- The cvRoberts_dns.c file can be found in the examples directory of the SUNDIALS module. To access it, run the following in your working directory:
cp /usr/local/pacerepov1/sundials/2.5.0/gcc-4.9.0/examples/cvode/serial/cvRoberts_dns.c .
- PBS Script can be found here
- You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.
Part 1: The PBS Script¶
#PBS -N sundialsTest #PBS -l nodes=1:ppn=2 #PBS -l pmem=2gb #PBS -l walltime=3:00 #PBS -q force-6 #PBS -j oe #PBS -o sundialsTest.out cd $PBS_O_WORKDIR module load gcc/4.9.0 module load lapack/3.6.0 module load sundials/2.5.0 gcc -lsundials_cvode -lsundials_nvecserial -lm -llapack -lblas cvRoberts_dns.c ./a.out > result.out
#PBSdirectives are standard, requesting 3 minutes of walltime and 1 node with 2 cores. More on
#PBSdirectives can be found in the PBS guide
$PBS_O_WORKDIRis a variable that represents the directory you submit the PBS script from. Make sure the files you want to use are in the same directory you put the PBS script.
- Output Files will also show up in this dir as well
module load sundials/2.5.0loads the 2.5.0 version of SUNDIALS. To see what versions of a software are available, run
module avail [Software], and load the one you want. The other modules are dependencies that must be loaded before SUNDIALS is loaded.
gcc -lsundials_cvode -lsundials_nvecserial -lm -llapack -lblas cvRoberts_dns.cwill compile the cvRoberts_dns.c file using the specified libraries passed in with the -l flag.
./a.out > result.outwill print the output of running the program to result.out.
Part 2: Submit Job and Check Status¶
- Make sure you're in the dir that contains the
PBSScript as well as the
- Submit as normal, with
qsub <pbs script name>. In this case
- Check job status with
qstat -t 22182721, replacing the number with the job id returned after running qsub
- You can delete the job with
qdel 22182721, again replacing the number with the jobid returned after running qsub
Part 3: Collecting Results¶
- In the directory where you submitted the
PBSscript, you should see a
sundialsTest.outfile which contains the results of the job and
results.outwhich contains the resulting output from compiling
cator open the file in a text editor to take a look.
sundialsTest.outshould just have the PBS Prologue at the top and the PBS Epilogue at the bottom with nothing in between.
results.outshould look like this:
3-species kinetics problem At t = 2.6391e-01 y = 9.899653e-01 3.470564e-05 1.000000e-02 rootsfound = 0 1 At t = 4.0000e-01 y = 9.851641e-01 3.386242e-05 1.480205e-02 At t = 4.0000e+00 y = 9.055097e-01 2.240338e-05 9.446793e-02 At t = 4.0000e+01 y = 7.158017e-01 9.185037e-06 2.841892e-01 At t = 4.0000e+02 y = 4.505360e-01 3.223271e-06 5.494608e-01 At t = 4.0000e+03 y = 1.832299e-01 8.944378e-07 8.167692e-01 At t = 4.0000e+04 y = 3.898902e-02 1.622006e-07 9.610108e-01 At t = 4.0000e+05 y = 4.936383e-03 1.984224e-08 9.950636e-01 At t = 4.0000e+06 y = 5.168093e-04 2.068293e-09 9.994832e-01 At t = 2.0790e+07 y = 1.000000e-04 4.000397e-10 9.999000e-01 rootsfound = -1 0 At t = 4.0000e+07 y = 5.202440e-05 2.081083e-10 9.999480e-01 At t = 4.0000e+08 y = 5.201061e-06 2.080435e-11 9.999948e-01 At t = 4.0000e+09 y = 5.258603e-07 2.103442e-12 9.999995e-01 At t = 4.0000e+10 y = 6.934511e-08 2.773804e-13 9.999999e-01 Final Statistics: nst = 542 nfe = 755 nsetups = 107 nfeLS = 0 nje = 11 nni = 751 ncfn = 0 netf = 22 nge = 570
- After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
- Congratulations! You successfully ran SUNDIALS on the cluster.