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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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carveme and cplex academic version #113

Closed ghost closed 3 years ago

ghost commented 3 years ago

Hello, could someone confirm that carveme is working with cplex academic version (I am not sure if "academic" means full version, it seems impossible to find this any cplex documentation) on a mac (python 3.8)? I have tried all solutions already posted, but I keep getting "cplex.exceptions.errors.CplexSolverError: CPLEX Error 1016: Community Edition. Problem size limits exceeded". Thank you so much in advance

cdanielmachado commented 3 years ago

Hi, Community Edition and Academic version are different things.

With pip install cplex you obtain the community edition, which limits problems to 1000 variables, and is not sufficient to run CarveMe.

You need to install the FULL version, which you can obtain for free with an academic license from IBM, and needs to be manually downloaded and installed from the IBM website.

ghost commented 3 years ago

Thanks for your fast answer, I was referring exactly to the cplex manually downloaded and installed as so called full version (not with pip or pip3). I will address the question to IBM. I really need carveme, thanks for building it!

cdanielmachado commented 3 years ago

Maybe you still have the community edition installed and it is using that one instead. You can try to pip uninstall cplex just to be sure.

ghost commented 3 years ago

Problem solved! For some reason, new accounts at IBM Academic Initiative get assigned a community version of CPLEX. I complained to IBM (everyone, use helpdesk for debugging!) and finally I got the good package. Thank you so much again!

ntromas commented 3 years ago

Hi! I got a similar issue. Still waiting for IBM to solve it...

ghost commented 3 years ago

Unfortunately I cannot share with you the CPLEX package I got from IBM, what I can share is that you should NOT use the link provided by Xavier Nodet (https://community.ibm.com/community/user/datascience/blogs/xavier-nodet1/2020/07/09/cplex-free-for-students?CommunityKey=ab7de0fd-6f43-47a9-8261-33578a231bb7&tab). Make a new account at "https://www.ibm.com/academic/home", login and get to the Academic Initiative cloud. Contact "cos-ai-support@wwpdl.vnet.ibm.com", they answer within 24h. Please, leave here a message if it works! Many people get now to use CarveMe and I think this important for #cdanielmachado!

ntromas commented 3 years ago

Interesting...I just wrote them. I was in contact with sales agent but apparently free/academic/trial versions don't have IBM support. I guess another option is to install Cplex 12.8 or 12.9? However, not sure how it works with Python 3.7 or 3.8 and not sure how to find the part numbers (https://www-03.ibm.com/isc/esd/dswdown/searchPartNumberResults.wss)

ghost commented 3 years ago

Absolutely not true what the sales agent said! IBM offers support for all products, moreover they keep track of all registrations through Academic Initiative. You can also call your local representative of IBM (I was almost to call them!) CPLEX from Academic Initiative works perfect on both python 3.7 and 3.8 (as well on 2.7). Installation goes well on BigSur too. Remember to uninstall any community edition (in BigSur go deep into the /opt/ and /lib/, remove manually any cplex related file including aliases).

ntromas commented 3 years ago

Do you have the name of the bin file? I got an answer from them and I have downloaded the version online: IBM ILOG CPLEX Optimization Studio 20.10 for Linux x86-64 (CC8ATML ). This version worked. python -c 'import cplex; print(cplex.version)' 20.1.0.0

ghost commented 3 years ago

Indeed for Linux is ILOG_COS_20.10_LINUX_X86_64.bin; Macos: IBM_ILOG_COS_20.10_OSX.zip; Win: ILOG_CPLEX_OS_20.10_WIN_X86_64.exe; and all the guides in ILOG_CPLEX_OPT_STUDIO_20.10_QSG.zip.