Building LCModel

martin · February 22, 2021, 8:14pm

Dear all,

Following the release of the LCModel source code I was able to get a successful build on Ubuntu 20.04 gcc version 9.3.0.

First step is to install gfortran if you don’t already have it:

sudo apt install gfortran

download the source code from: LCModel's home page and unzip:

unzip source.zip -d lcmodel_src
cd lcmodel_src

patch the code to overlook a failing internal check, “ILLOGICAL INITIA 5” - see LCModel manual, compile and link:

sed '2429d' LCModel.f > LCModel_patched.f
gfortran -c -fno-backslash -fno-f2c -ffast-math -O2 -ffpe-summary=none -Wuninitialized -std=legacy -fall-intrinsics LCModel_patched.f
gfortran -s -static LCModel_patched.o -o lcmodel

If all was successful the lcmodel binary will be available in the current directory and ready to be used in the normal way, eg:

./lcmodel < your_control_file

Compared to the provided example Makefile, it was necessary to add the -ffpe-summary=none flag to remove some non-important (according to google) runtime warnings and -std=legacy to demote a compilation error to a warning.

I did notice some very minor numerical differences between my compiled version and the one available on the website, so it’s probably better to use the prebuilt binary unless you have a good reason not to. The prebuilt binary is also much smaller than I was able to achieve for some reason - perhaps a different compiler was used.

The only requirement of gfortran means a Mac OS build may be possible once gfortran has been installed (eg brew install gcc).

Please share your successes and failures with building LCModel on your platform!

Martin

admin · February 22, 2021, 9:46pm

I’ve successfully built the lcmodel binary on MacOS Catalina using the following steps:
EDIT: Updated the instructions in this post to reflect changes made after the excellent suggestions by @martin and @dave below!

Download and install the gfortran compiler (https://github.com/fxcoudert/gfortran-for-macOS/releases/download/10.2/gfortran-10.2-Catalina.dmg), versions for other MacOS systems available here.
Download and unzip the source code, enter the directory.
Compile and link:

gfortran -c -fno-backslash -fno-f2c -O3 -fall-intrinsics -std=legacy -Wuninitialized -ffpe-summary=none LCModel.f
gfortran LCModel.o -o lcmodel

Run a control file (I used the LCModel test control file that I copied from the Linux machine, but I haven’t run the makebasis on the test basis set, so there is no basis set and an error results in the final test run):

./lcmodel < /Users/Georg/Documents/lcmodel/test/control/test.control

@martin , want to compare one of your test datasets to see what the numerical differences are?

Cheers,
Georg

martin · February 23, 2021, 5:18am

Hi @admin,

That’s great news. I’ve attached some test data and results from my local build and the “official” Linux build for comparison.

time for i in {1..10}; do lcmodel < ./control.file; done

is taking about 20s for both builds on my laptop. Would be very interesting to benchmark on M1 silicon.

test_lcm.zip (187.1 KB)

Martin

admin · February 23, 2021, 2:05pm

Hi @martin,

Thanks for the test data! Runs like a charm.
Took 19s on my 2017 MacBook (3.1 GHz i5). I do get a warning, but it doesn’t break the execution:

Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

I’m also attaching the resulting .coord file:
out.coord (30.1 KB)

This is quite exciting, I must say!
Georg

admin · February 23, 2021, 2:10pm

For MATLAB users, @Helge has previously written a script automating the generation of LCModel .control files. It is part of the Osprey software and can be found in the Osprey GitHub repository, but it is currently rather tailored to recreating an Osprey analysis in LCModel. Maybe it’s helpful for someone who wants to set up their own LCModel wrapper and batch-analyse their data on their local machine.

martin · February 23, 2021, 2:16pm

First Mac OS LCModel fit, maybe, nice! Seems numerically closer to the Ubuntu build.

I had the same runtime warnings, (which are apparently nothing to be concerned about) and was able to remove them with:

-ffpe-summary=none

perhaps support for this flag was dropped in more recent versions of gcc?

I also tweaked the patch line in my first post to remove the line of LCModel source code - probably being overcautious though.

Martin

admin · February 23, 2021, 2:28pm

Excellent! Adding -ffpe-summary=none to the compile command removed the warnings here as well. Thanks!

dave · February 23, 2021, 3:12pm

I had an older version (8.2) of gfortran lying around and managed to get it to compile on my 9 years old Macbook Pro with a combination of Martin’s and Georg’s instructions:

gfortran -c -fno-backslash -fno-f2c -O2 -ffpe-summary=none -std=legacy -Wuninitialized -fall-intrinsics LCModel_patched.f

gfortran LCModel_patched.o -o lcmodel

since there aren’t statically linked library versions. The -fallow-argument-mismatch isn’t an option for the older compiler.

@martin, your for loop takes just over 22 seconds on my 2.3 GHz i7 Macbook Pro. I tried compiling with/without the fast-math option. With gives the same concs as your Ubuntu build, without gives the same concs as you reference build.

Cheers,
Dave

out2.pdf (24.7 KB)

martin · February 23, 2021, 4:10pm

Thanks @dave - I had a suspicion changing one of the compiler flags might fix the failing internal test and removing -ffast-math seems to do the trick on my system.

So hopefully no more need for the patch, just:

gfortran -c -fno-backslash -fno-f2c -O3 -ffpe-summary=none -Wuninitialized -std=legacy -fall-intrinsics LCModel.f
gfortran LCModel.o -o lcmodel

works for me. Removing the fast-math flag doesn’t seem to hurt performance and O3 optimisation got the loop benchmark down to 17 seconds

Martin

admin · February 23, 2021, 4:24pm

Thanks both, this is awesome. Indeed this removes the need to patch the .f file, and the exact same list of commands can be run for Ubuntu and Catalina. I’m updating my post above accordingly.

PGMM · February 23, 2021, 9:14pm

Thanks MRS nerds!! I will see if I can wrangle some time this week to give it a try myself.

admin · February 23, 2021, 9:20pm

LCMullins! Good luck!

martin · February 24, 2021, 9:18am

So I got a bit suspicious of all the compiler flags provided in the example Makefile after the problems with -ffast-math. A more minimal build command is simply:

gfortran -ffpe-summary=none -std=legacy -O3 LCModel.f -o lcmodel

My Windows box had gfortran (8.3.0) installed for R development and:

gfortran.exe -ffpe-summary=none -std=legacy -O3 LCModel.f -o LCModel.exe

works fine. Actually better than fine, the benchmark for the windows build from the LCModel website took 22 seconds, whereas the locally compiled version took 12.5s on an AMD Ryzen 5 3600. It’s possible the “official” build works better with Intel.

So close to a sub-second analysis!

Martin

chris · February 24, 2021, 7:04pm

Thanks everyone for sharing these instructions. BTW… I registered lcmodel · GitLab in case it will be useful to host the lcmodel code moving forwards.

bsoher · February 24, 2021, 8:09pm

Hi Everyone,

Just another data point. I downloaded and compiled on Win10 gfortran 7.3 (which I had already installed for another project). Used Martin’s shorter compile line:

gfortran.exe -ffpe-summary=none -std=legacy -O3 LCModel.f -o LCModel.exe

Compile time was about 29 sec on an older intel i7-6900k 3.2 GHz. Used Martin’s test data.

Quick aside … this was the first time I ever ran LCModel in my life! Really.

Did a quick loop x10 and got 19.01 sec processing time. Results similar to ref and Ubuntu though I haven’t look extremely closely at all the table entries.

Best,

Brian.

PS. Does anyone know what brought about this change in events with Steven?

bsoher · February 25, 2021, 1:33am

This one’s for Martin … I took the afternoon to geek out a bit. Ran out this bit of Python code and managed to process 20 data files in 12.39 seconds for an average processing time of 0.62 sec! Admittedly, it was just your test data copied to 20 different file names … but still nice to see.

Enjoy,

Brian.

import time
import multiprocessing
import subprocess

def calculate(idx):

    lines = []
    lines.append("$LCMODL")
    lines.append("key=210387309")
    lines.append("nunfil=1024")
    lines.append("deltat=5e-04")
    lines.append("hzpppm=127.786142")
    lines.append("filbas='3t.basis'")
    lines.append("filraw='data"+idx+".raw'")
    lines.append("filps='out"+idx+".ps'")
    lines.append("$END")
    msg = '\n'.join(lines)
    msg = msg.encode('utf-8')

    proc = subprocess.Popen(
        ['LCModel.exe',],        
        shell=True,
        stdin=subprocess.PIPE,
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
    )
    stdout_value, stderr_value = proc.communicate(msg)
    return idx+'_done'


def pipe_lcm_multi():
    
    t0 = time.time()
    
    pool = multiprocessing.Pool(None)
    tasks = [str(i) for i in range(20)]
    results = []
    r = pool.map_async(calculate, tasks, callback=results.append)
    r.wait() # Wait on the results
    print(results)

    t1 = time.time()
    print('time = ',str(t1-t0))


#--------------------------------------------------------------------
# Test Code

if __name__ == '__main__':
    """
    Copied data.raw to data1.raw, data2.raw ... data19.raw
    and added control.file values into the string list above

    Results on i7-6900k, 8 cores, 16 threads was 12.39 sec
    for 20 files, or 0.62 sec each
    """
    pipe_lcm_multi()

martin · February 25, 2021, 8:57am

Thanks @bsoher! Could you bump up the runs to 64 and run again on an AMD 64-Core Threadripper 3990X for me .

Comped to the historic cost of of the license - a ‎£3.5k desktop CPU is not as crazy at is sounds for LCModel users.

alex · February 25, 2021, 5:52pm

Martin, thanks very much for the build instructions.

Two further comments:

Line 2500 of lcmodel.f, add a line reading go to 200 to bypass the license check altogether, and obviate the need for adding the master key to your .control files.

Regarding numeric differences, I just ran the full public Big GABA dataset through a local build (Debian 9.1, gfortran 6.3.0-18+deb9u1), I’d say it agrees pretty well in this instance Of course this may well differ according to library versions…

(N=222, total processing time 8.65 seconds with a bit of parallelisation: it’s fast)

lcm

alex · February 25, 2021, 5:57pm

The other part of that comparison… lcm_ba

martin · February 26, 2021, 9:17am

Hi @alex,

My first rough check for consistency with the “official” build on the LCModel website was with the -ffast-math flag and I saw some minor differences. @dave later spotted that removing this flag gave better agreement with the official build.

Thanks for doing a more rigorous check. Did you use the -ffast-math flag?

Martin