Re: fit is slow due to missing/wrong shared libraries?

Hi Robin,

You should first run a CPU benchmark on both systems to get a baseline. AMD might be significantly slower than Intel.


Cheers,
Werner
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On 19 Apr 2024, at 15:23, Garcia Victoria, Robin <[email protected]> wrote:

Hello everyone,

I have installed gnuplot 5.0.5 on a VM (on Debian 9) and gnuplot 5.4.4 (Debian 12) in a Singularity container.

The runtimes differ considerably:

On the VM with gnuplot version 5.0.5
real 0m31.142s
user 0m14.280s
sys 0m15.672s

In the container with gnuplot version 5.4.4
real 2m32.341s
user 1m31.325s
sys 1m0.593s

My specs are:
- VM: AMD EPYC 7543P 32-Core Processor and 32GB RAM
- Singularity: Intel(R) Xeon(R) Gold 6154 CPU @ 3.00GHz (72-Core) and 378GB RAM

root@rie-ex-web160,tmp: cat fit_run_gnuplottestlauf_year1950
Set terminal postscript
set output "Inbreeding_log_gnuplottestlauf_year1950.ps"
set ylabel "Coefficient" font "Times-Italic,14"
set xlabel "Days of birth" font "Times-Italic,14"
set style line 1 lt 1 lw 15
set button below
set autoscaling xy
f(x)=a*x+b
FIT_LIMIT =1E-20
fit f(x) "Inbreeding_log_gnuplottestlauf_year1950.csv" u 1:2 via a,b
Plot "Inbreeding_log_gnuplottestlauf_year1950.csv" with 1:2 title "Log of Inbreed Coeff", f(x)

root@rie-ex-web160,tmp: cat Inbreeding_log_gnuplottestlauf_year1950.csv
1 0.0000000000000000 1950
21 0.0000000000000000 1950
73 0.0000000000000000 1950
265 0.0000000000000000 1950

I have checked which shared libraries are used by gnuplot (ldd /usr/bin/gnuplot).

Apptainer>
ldd /usr/bin/gnuplot | wc -l
84

root@rie-ex-web160,~: ldd /usr/bin/gnuplot | wc -l
46

My container, where the fitting with gnuplot runs slower than in the VM, has 84 shared libraries for gnuplot, while 46 shared libraries are used by gnuplot in the VM.

Could this be the reason why the fitting is significantly slower?

I would be grateful for any tips and advice.

Best

Robin

Robin Garcia Victoria (M.Sc.)
Computer scientist
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Friedrich-Loeffler-Institut
Bundesforschungsinstitut für Tiergesundheit
Federal Research Institute for Animal Health
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