lrslib on CentOS 7

[maxEntropyProd]

This is an OS issue and not ecmtool, but if you have a quick answer, that would be great. I'm trying to run ecmtool on a CentOS 7 box, but I can't find any repo for lrslib, so I grabbed the source from here http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/ and have a redund executable, but when I run the ecmtool example "python main.py --model_path models/e_coli_core.xml --auto_direction true --out_path core_conversions.csv"

ecmtool errors with this from redund:

Iteration 24/25
Adding 8 candidates
Removing 6 rays

Running redund

*lrs:overflow possible: restarting with 128 bit arithmetic

Traceback (most recent call last):
  File "main.py", line 297, in <module>
    remove_infeasible=args.remove_infeasible)
  File "/home/jvallino/Software/ecmtool/ecmtool-master/ecmtool/network.py", line 409, in compress
    remove_infeasible=remove_infeasible)
  File "/home/jvallino/Software/ecmtool/ecmtool-master/ecmtool/network.py", line 444, in compress_inner
    self.cancel_clementine(verbose=verbose)
  File "/home/jvallino/Software/ecmtool/ecmtool-master/ecmtool/network.py", line 702, in cancel_clementine
    self.output_metabolite_indices())
  File "/home/jvallino/Software/ecmtool/ecmtool-master/ecmtool/network.py", line 103, in clementine_equality_compression
    G = redund(G, verbose=verbose)
  File "/home/jvallino/Software/ecmtool/ecmtool-master/ecmtool/helpers.py", line 275, in redund
    matrix_nored = np.append(matrix_nored, [row], axis=0)
  File "<__array_function__ internals>", line 6, in append
  File "/home/jvallino/Software/ecmtool/ecmtool-master/python3-virtualenv/lib64/python3.6/site-packages/numpy/lib/function_base.py", line 4671, in append
    return concatenate((arr, values), axis=axis)
  File "<__array_function__ internals>", line 6, in concatenate
ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 54 and the array at index 1 has size 8

I've tried using versions lrs version 71a and 71b, which generate the above, and version 72 generates a syntax like error. Assuming I'm doing this correctly (probably not), what version of lrslib does ecmtool use?

thanks! -joe

[tjclement]

Hi Joe,

More recent versions of lrslib should be expected to work with ecmtool, so this is something we'll have to investigate and fix.

To help you out quickly now: at time of development of ecmtool I believe the version of lrslib that was available on debian-like distributions was 0.62. You can find it here: https://packages.ubuntu.com/bionic/amd64/lrslib/download. You can compile 0.62 yourself as you did with the other versions: http://cgm.cs.mcgill.ca/~avis/C/lrslib/archive/lrslib-062.tar.gz. Alternatively you can convert the Ubuntu .deb package to .rpm using something like this: https://linuxconfig.org/how-to-install-deb-file-in-redhat-linux-8. Then you can just install the prebuilt package.

[maxEntropyProd]

Thanks Tom!! I'll let you know what I find. -joe

[maxEntropyProd]

I used lrslib-062.tar.gz version with "make all" and that worked! Newer versions must have some change in input arguments?