Install Request: Install NONMEM 7.5 if the UCL license allows [IN06144843]

[balston]

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.

[balston]

I've emailed Icon asking about getting hold of the NONMEM 7.5 installer archive.

[balston]

Looks like I have the install and download instructions for NONMEM 7.5. I will look further into it on Monday.

[balston]

I now have the NONMEM751.zip installer archive and the password necessary to unzip it.

[balston]

I've uploaded it to ~ccaabaa/Scratch/NONMEM/ on both Myriad and Kathleen.

[balston]

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.

[balston]

The original build of NONMEM was documented here https://github.com/UCL-RITS/research-computing/issues/376

[balston]

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

[balston]

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/

[balston]

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.

[balston]

There are three files that need changing/adding to the util or run directories. util:

mpiloc-setup
nmfe75

and run:

nmfe75
parafile.sh