Install Request: Install NONMEM 7.5 if the UCL license allows [IN06144843]
Opened this issue · 21 comments
Request to install NONMEM 7.5 on Myriad and Kathleen.
Commercial software supplied by Icon Inc from the USA. https://www.iconplc.com/solutions/technologies/nonmem/
UCL license owned by the School of Pharmacy.
Need to check how and if we can get the new version from Icon Inc.
I've emailed Icon asking about getting hold of the NONMEM 7.5 installer archive.
Looks like I have the install and download instructions for NONMEM 7.5. I will look further into it on Monday.
I now have the NONMEM751.zip installer archive and the password necessary to unzip it.
I've uploaded it to ~ccaabaa/Scratch/NONMEM/ on both Myriad and Kathleen.
The Linux unzip command can handle the password protected zip archive so the NONMEM 7.5.1 installer is now in:
/home/ccspapp/Scratch/Software/NONMEM/nm751CD
on both Myriad and Kathleen.
The original build of NONMEM was documented here https://github.com/UCL-RITS/research-computing/issues/376
Myriad
First attempt. Install NONMEM using the default Intel compilers and MPI. So looking at the current installation instructions and how we did the old version trying as ccspapp:
module load compilers/intel/2018/update3
module load mpi/intel/2018/update3/intel
cd Scratch/Software/NONMEM/nm751CD
cp /shared/ucl/apps/NONMEM/nm730_Intel/nonmem.lic .
./SETUP75 /home/ccspapp/Scratch/Software/NONMEM/nm751CD /shared/ucl/apps/NONMEM/nm751_Intel ifort y ar same rec i unzip nonmem75e.zip nonmem75r.zip
I ran the install twice because the first time it didn't have a valid license file so the build test failed. The second time seems to have worked:
Building NONMEM Executable
Starting nonmem execution ...
License Registered to: University College London RITS
Expiration Date: 14 MAR 2024
Current Date: 20 SEP 2023
Days until program expires : 179
First Order
MONITORING OF SEARCH:
0ITERATION NO.: 0 OBJECTIVE VALUE: 110.244033888713 NO. OF FUNC. EVALS.: 6
CUMULATIVE NO. OF FUNC. EVALS.: 6
NPARAMETR: 3.0000E+00 8.0000E-02 4.0000E-02 6.0000E+00 5.0000E-03 3.0000E-01 2.0000E-04 6.0000E-03 4.0000E-01 4.0000E-01
PARAMETER: 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01 1.0000E-01
GRADIENT: 1.4640E+01 -1.6691E+01 5.6460E+01 -9.4129E+00 -1.1699E+01 1.0623E+01 -6.3485E-01 -4.7803E+01 -9.6457E+00 5.2414E+00
0ITERATION NO.: 5 OBJECTIVE VALUE: 105.453693542211 NO. OF FUNC. EVALS.: 39
CUMULATIVE NO. OF FUNC. EVALS.: 45
NPARAMETR: 2.8166E+00 8.0433E-02 3.8563E-02 6.6123E+00 9.7862E-03 -3.9509E-02 2.3438E-04 8.1375E-03 4.9657E-01 4.0346E-01
PARAMETER: -5.3055E-02 1.0703E-01 5.7598E-02 1.4858E-01 1.8644E-01 -1.2545E-02 1.5794E-01 1.3452E-01 3.7714E-02 1.0431E-01
GRADIENT: 3.5103E-01 -1.3214E+01 2.8003E+01 1.1115E+00 1.9193E+00 -5.3252E+00 7.1534E-02 -2.2091E+01 -1.4424E+00 8.2329E+00
0ITERATION NO.: 10 OBJECTIVE VALUE: 104.747694492991 NO. OF FUNC. EVALS.: 35
CUMULATIVE NO. OF FUNC. EVALS.: 80
NPARAMETR: 2.7362E+00 7.6935E-02 3.5982E-02 5.7362E+00 1.0840E-03 -2.9208E-01 2.3701E-04 9.4013E-03 5.1805E-01 3.8850E-01
PARAMETER: -1.1928E-01 4.9234E-02 -2.3022E-02 7.7517E-02 2.2173E-02 -9.9574E-02 1.9498E-01 1.4956E-01 -1.7173E-01 8.5414E-02
GRADIENT: -1.3933E+00 -7.4632E+00 9.3144E+00 1.0280E+00 9.6395E-01 -3.1313E+00 1.0212E+00 -5.3784E+00 -2.0828E+00 -9.1477E-01
0ITERATION NO.: 15 OBJECTIVE VALUE: 104.561085415242 NO. OF FUNC. EVALS.: 36
CUMULATIVE NO. OF FUNC. EVALS.: 116
NPARAMETR: 2.7735E+00 7.8097E-02 3.6292E-02 5.5466E+00 5.1735E-03 -1.2911E-01 2.3941E-04 9.0947E-03 5.1461E-01 3.8752E-01
PARAMETER: -8.8567E-02 6.8686E-02 -1.2994E-02 6.0711E-02 1.0762E-01 -4.4762E-02 1.9028E-01 1.4643E-01 -8.4016E-02 8.4157E-02
GRADIENT: 7.7937E-03 5.7189E-03 3.0426E-02 -5.1648E-03 -1.2939E-02 1.4490E-02 7.4602E-04 -2.5227E-02 -3.1443E-03 1.5799E-02
0ITERATION NO.: 19 OBJECTIVE VALUE: 104.561066311468 NO. OF FUNC. EVALS.: 33
CUMULATIVE NO. OF FUNC. EVALS.: 149
NPARAMETR: 2.7739E+00 7.8129E-02 3.6307E-02 5.5498E+00 5.2393E-03 -1.2767E-01 2.3985E-04 9.1064E-03 5.1521E-01 3.8750E-01
PARAMETER: -8.8304E-02 6.9219E-02 -1.2510E-02 6.0998E-02 1.0895E-01 -4.4249E-02 1.9095E-01 1.4652E-01 -8.3269E-02 8.4127E-02
GRADIENT: 1.2144E-04 -1.4882E-04 -6.6266E-06 -7.5745E-05 -1.6157E-05 1.1307E-04 6.4128E-05 1.1193E-04 -1.7655E-05 4.2678E-05
Elapsed estimation time in seconds: 0.07
Elapsed covariance time in seconds: 0.04
Elapsed postprocess time in seconds: 0.02
Elapsed finaloutput time in seconds: 0.04
Done with nonmem execution
You should now compare REPORT5.txt vs. REPORT5IDS.txt
Values should be similar.
E.g., the following should be identical:
grep #OBJV: REPORT5.txt
#OBJV:******************************************** 104.561 **************************************************
grep #OBJV: REPORT5IDS.txt
#OBJV:******************************************** 104.561 **************************************************
The following path was selected for ifort: /shared/ucl/apps/intel/2018.Update3/compilers_and_libraries_2018.3.222/linux/bin/intel64/
The following path was selected for link: /usr/bin/
Need to use the parafile.sh from the NONMEM 7.3 installation for parallel runs using Grid Engine and possibly some of the other set up files.
There are three files that need changing/adding to the util or run directories. util:
mpiloc-setup
nmfe75
and run:
nmfe75
parafile.sh
As ccspapp:
cd /shared/ucl/apps/NONMEM/nm751_Intel/util
cp ~ccaabaa/Scratch/Software/NONMEM/mpiloc-setup .
cp ~ccaabaa/Scratch/Software/NONMEM/nmfe75 .
cd ../run
cp ~ccaabaa/Scratch/Software/NONMEM/nmfe75 .
cp ~ccaabaa/Scratch/Software/NONMEM/parafile.sh .
Now to try running a test parallel job.
Forgot something - need a module file.
Module file done and test job submitted:
job-ID prior name user state submit/start at queue slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
464106 0.00000 NONMEM_Int ccaabaa qw 09/27/2023 17:33:45 12
I made a mistake in the module file prereqs which I think I've fixed. Test job resubmitted.
Test job has worked using a job script like this:
#!/bin/bash -l
# Batch script to run a MPI NONMEM job on Myriad
# NONMEM Version 7.5.1 Intel Fortran Compiler with Intel MPI 2018 Update 3
# 1. Force bash as the executing shell.
#$ -S /bin/bash
# 2. Request ten minutes of wallclock time (format hours:minutes:seconds).
# Change this to suit your requirements.
#$ -l h_rt=0:10:0
# 3. Request 1 gigabyte of RAM. Change this to suit your requirements.
#$ -l mem=1G
# 3a. Request 15 gigabyte of TMPDIR space (default is 10 GB)
#$ -l tmpfs=15G
# 4. Set the name of the job. You can change this if you wish. Also set the
# project on the OS Upgrade dev cluster.
#$ -N NONMEM_Intel_MPI_job_12
# 5. Select the MPI parallel environment and 12 processes.
#$ -pe mpi 12
# 6. Set the working directory to somewhere in your scratch space. This is
# a necessary step with the upgraded software stack as compute nodes cannot
# write to your $HOME.
#
# NOTE: this directory must exist.
#
# Replace "<your_UCL_id>" with your UCL user ID :)
#$ -wd /home/<your_UCL_id>/Scratch/NONMEM_examples
# 7. Setup unique directory for this job
jobDir=example1_parallel_$JOB_ID
mkdir $jobDir
# 8. Copy control and datafiles to jobDir
cp foce_parallel.ctl $jobDir
cp example1b.csv $jobDir
cd $jobDir
# 9. Run your NONMEM program.
# Load modules - currently need 2018 Intel modules which are the default
module load nonmem/7.5.1/intel-2018-update3
# 10. Create parafile for job using $TMPDIR/machines
parafile.sh $TMPDIR/machines > example1.pnm
#11. Run NONMEM
nmfe75 foce_parallel.ctl example1.res -parafile=example1.pnm -background -maxlim=2 > example1.log
Kathleen
As ccspapp:
module load compilers/intel/2018/update3
module load mpi/intel/2018/update3/intel
cd ~/Scratch/Software/NONMEM/nm751CD
cp /shared/ucl/apps/NONMEM/nm730_Intel/nonmem.lic .
./SETUP75 /home/ccspapp/Scratch/Software/NONMEM/nm751CD /shared/ucl/apps/NONMEM/nm751_Intel ifort y ar same rec i unzip nonmem75e.zip nonmem75r.zip
Installation completed and serial test worked.
Now updating set up files (same as on Myriad):
cd /shared/ucl/apps/NONMEM/nm751_Intel/util
cp ~ccaabaa/Scratch/Software/NONMEM/mpiloc-setup .
cp ~ccaabaa/Scratch/Software/NONMEM/nmfe75 .
cd ../run
cp ~ccaabaa/Scratch/Software/NONMEM/nmfe75 .
cp ~ccaabaa/Scratch/Software/NONMEM/parafile.sh .
Test 2 node (80 core) job submitted.
80 core test job worked.
user informed about Kathleen installation.