ATS installation error: Could NOT find BLAS (missing: BLAS_LIBRARIES)
Rathore, Saubhagya
Dear ATS developers and users,
I am having trouble installing ATS on my MacBook. I am getting the error “Could NOT find BLAS (missing: BLAS_LIBRARIES)”. I tried a few versions of CommandLineTools ranging from the latest (version: 15.0) to some older versions (14.3XX). I made sure that openblas is installed (brew install openblas).
I have attached CMakeOutput.log and CMakeError.log. Any help or tips will be appreciated.
System details:
Chip Apple M1 Max
macOS Ventura 13.5
ATS details:
Branch master
Thanks
Saubhagya
Lipnikov, Konstantin
Sent: Friday, November 3, 2023 1:36 PM
To: ats-...@googlegroups.com <ats-...@googlegroups.com>
Subject: [EXTERNAL] ATS installation error: Could NOT find BLAS (missing: BLAS_LIBRARIES)
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Coon, Ethan
I think he already did downgrade CommandLineTools (I’ve had the same problem with 15.0).
This is failing on configure of TPLs. Saubhagya, can you run bootstrap with –debug_find_blas, forward the output to a file, and also send that? David might be able to discern where that is failing. It didn’t look like it was looking in the right places for Apple to me, but I didn’t have this problem with 13.3.
Ethan
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Rathore, Saubhagya
Thanks, Konstantin and Ethan, for your suggestions. Here is what I have in CMakeCache.txt (attached to this email).
//Path to a library.
BLAS_openblas_LIBRARY:FILEPATH=BLAS_openblas_LIBRARY-NOTFOUND
I removed Xcode and tried CommandLineTools 14.1 and 14.3.1. I can try a few more versions.
The output from the bootstrap with –debug_find_blas flag is attached to this email (output.log).
Thank you for your help.
Regards
Sauhbagya
Coon, Ethan
You’re seeing NOTFOUND because it is failing while trying to find it. That is the default “not initialized” value. So that is expected.
Ethan
Rathore, Saubhagya
I see. I wonder if openblas installed by homebrew is causing the problem. I did try without it and still got the same error.
Regards
Saubhagya
Rathore, Saubhagya
Dear all,
The openblas-related problem was fixed by removing the XCode and using CommandLineTools version 14.3. However, now I am getting errors while building Boost. So far, I have not been able to remedy it.
The Boost error log is attached. I would appreciate any ideas you might have.
“…/amanzi_tpls-build-master-Debug/boost/boost-timestamps/boost-configure-err.log”
Thanks
Saubhagya
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Coon, Ethan
Yuck, you have some inconsistency in clang, commandline tools, homebrew, and C++ standard.
Is it possible you have installed homebrew’s gcc compiler and are trying to use it with commandline tools standard libraries?
Personally, my next step would be to blow away homebrew, all xcode and CommandLineTools, then reinstall CommandLineTools v14.3, then reinstall homebrew, gfortran, and mpi (not blas), then try again. There may be a less time-intensive fix, but I’m not sure what it is.
Ethan
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Rathore, Saubhagya
Yes, it seems like that is the issue. when I look into boost-configure-out.log I see the message below. Time to start with a clean slate.
Building B2 engine..
A C++11 capable compiler is required for building the B2 engine.
Toolset 'clang' does not appear to support C++11.
> clang++ -x c++ -std=c++11 check_cxx11.cpp
> clang++ -x c++ -std=c++11 check_cxx11.cpp
Failed to build B2 build engine
Rathore, Saubhagya
Removing CommandLineTools, Homebrew (and all related packages), and reinstalling (in the order) CommandLineToolsV14.3, gfortran, open-mpi, and cmake did not help. Boost is still having conflicts with Clang libraries.
I also tried hacking amanzi/config/SuperBuild/include/Build_Boost.cmake to force it to use GCC from homebrew but that also did not work.
I will try reversing the order of installation of CommandLineTools and Homebrew (may not work as brew install might need CommandLineTools). If there are other ideas worth trying, I will be happy to try them.
Thanks
Saubhagya
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Moulton, J. David
I empathize with your frustration. These kind of strange incompatibilities related to XCode/command line tools are hard to resolve and sometimes seem to boil down to fundamental problems with either XCode or brew/macports.
What version of OSX are you running? For what it's worth I'm currently on XCode 14.2. on Monterey (12.7.1).
Note its always important to make sure that both the build and install directories are clean (empty) as cruft from previous failed attempts can really mess with fixes that would have worked.
For debugging boost related builds I go in and run the boost build manually and try to check all the specific paths (which compilers are really being used) and libraries that are being linked. But various incompatibilities do arise through the mpi configuration. So I typically build my own mpi. The mpi you installed is likely using the clang gcc/g++ but that's important to check because I'm pretty sure boost builds use the raw compilers not the mpi wrappers. So if somehow these are out of sync it can mess things up.
Hope this is helpful, happy to try to help more if needed.
Cheers, David
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Moulton, J. David
Also, worth testing the basics. I have a few hello-world type programs that I use to test compilers. I use both serial and mpi hello-world tests and sometimes it reveals the setup issue more clearly.
Cheers, David
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From: 'Moulton, J. David' via Amanzi-ATS Users <ats-...@googlegroups.com>
Sent: Wednesday, November 8, 2023 12:34 PM
To: Coon, Ethan; ats-...@googlegroups.com; Rathore, Saubhagya
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Rathore, Saubhagya
Hi David,
Thanks for the detailed reply. I am on macOS Ventura 13.5, so this could very well be the problem. Yes, the BLAS issue was resolved by downgrading CommandLineTools to v14.3; boost is where I am stuck. Yes, I delete all build and install directories before every new attempt.
Once I have exhausted all permutations and combinations of CommandLineTools versions and brew-installed packages, I will try building boost manually. I will see if there are any pending updates to macOS.
Best regards
Saubhagya
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Coon, Ethan
I’m confused by this statement:
- I also tried hacking amanzi/config/SuperBuild/include/Build_Boost.cmake to force it to use GCC from homebrew but that also did not work.
You should not have a gcc from homebrew, and if you do, that’s probably the problem.
You might have /usr/bin/gcc, which is actually clang, and you should have /opt/homebrew/bin/gfortran, but you should not have /opt/homebrew/bin/gcc.
Rathore, Saubhagya
Yes, you are right. I do have gcc from homebrew.
Rathore, Saubhagya
Sorry, the previous email got sent prematurely. Yes, I do have gcc from homebrew as well which might be causing the issue. Should I create softlink then?
(base) ➜ ~ which gcc
/opt/homebrew/bin/gcc
Thanks
Saubhagya
Rathore, Saubhagya
I may not be making too much sense here, but I will try. I cannot get rid of /opt/homebrew/bin/gcc as it is required by open-mpi. Any workaround for this?
Coon, Ethan
At some point you either manually or somehow in responding to a homebrew prompt, symlinked the Gnu C Compiler into /opt/homebrew/bin.
brew install gcc
without symlinking should have put gcc into a folder – for me, I have:
/opt/homebrew/Cellar/gcc/13.2.0/bin/gcc-13
AND
/opt/homebrew/bin/gcc-13 (a symlink to the first one)
But I do _not_ have /opt/homebrew/bin/gcc. You likely have a link from /opt/homebrew/bin/gcc to /opt/homebrew/Cellar/gcc/X.Y.Z/bin/gcc-X.
By symlinking gcc into /opt/homebrew/bin, when you installed open-mpi, it used that gcc, and so you likely have something like:
mpicc -show
gives:
??? -I/opt/homebrew/Cellar/open-mpi/4.1.5/include -L …
For me, ??? is clang
For you, it is probably either gcc or /opt/homebrew/bin/gcc?
You should be able to delete the symlink that you currently have, confirm that `which gcc` gives /usr/bin/gcc (which is really clang), then reinstall open-mpi. Then you should not see these conflicts of standard libraries, where you are trying to use the clang std library with the gcc compiler.
If starting fresh with a clobbered /opt/homebrew, `brew install gcc`; `brew install open-mpi` should not create /opt/homebrew/bin/gcc, leaving clang as your primary C/C++ compiler and as the compiler used by open-mpi.
Alternatively, there should also be a way to install the Gnu standard libraries and use Gnu std libraries with the gcc compiler you have. I’m not sure how to do that.
Moulton, J. David
Just to add a bit to Ethan's note. There have been attempts for the homebrew (and macports) mpi packages to use specific compilers, not just the system gcc (which on OSX is clang). It's possible that the openmpi you installed from homebrew was one that was built and intended for use with the homebrew gcc. It's also possible that this connection was made later and can be removed as Ethan suggests. Either way I think you're problems will be solved when you have a consistent setup for mpi and gcc.
Cheers, David
________________________________________
From: 'Coon, Ethan' via Amanzi-ATS Users <ats-...@googlegroups.com>
Sent: Tuesday, November 14, 2023 10:36 AM
To: Rathore, Saubhagya; ats-...@googlegroups.com
Thanks
Saubhagya
From: Rathore, Saubhagya <rath...@ornl.gov>
Date: Tuesday, November 14, 2023 at 11:26 AM
To: Coon, Ethan <coo...@ornl.gov>, ats-...@googlegroups.com <ats-...@googlegroups.com>
Subject: Re: ATS installation error: Could NOT find BLAS (missing: BLAS_LIBRARIES)
Yes, you are right. I do have gcc from homebrew.
From: Coon, Ethan <coo...@ornl.gov>
Date: Friday, November 10, 2023 at 9:57 AM
To: Rathore, Saubhagya <rath...@ornl.gov>, ats-...@googlegroups.com <ats-...@googlegroups.com>
Subject: Re: ATS installation error: Could NOT find BLAS (missing: BLAS_LIBRARIES)
I’m confused by this statement:
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Fengming Yuan
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Fengming Yuan
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Rathore, Saubhagya
Thanks everyone for the help. I clobbered /opt/homebrew and reinstalled homebrew, installed gfortran and openmpi. My which gcc is now /usr/local/bin/gcc, however when I do gcc –version, it points to homebrew.
My mpicc -show seems to be what we want to see:
clang -I/opt/homebrew/Cellar/open-mpi/4.1.6/include -L/opt/homebrew/Cellar/open-mpi/4.1.6/lib -L/opt/homebrew/opt/hwloc/lib -L/opt/homebrew/opt/libevent/lib -lmpi
Bootstrap fails when it tries to build cmake (log attached). This is because my cmake version is less than required.
When I try again after “brew install cmake”, bootstrap fails at boost building step.
Is this related to the issue Fengming pointed out?
Thanks
Saubhagya
Rathore, Saubhagya
So, finally, I was able to install ATS. I thought I would do a report-out to help others who may have similar issues.
My original issue was primarily due to BLAS libraries not being detected during the ATS installation process. The issue potentially arose because of some updates to XCode. This was resolved by removing XCode and downgrading CommandLineTools (to version 14.3).
My second issue appeared related to compiler inconsistencies (I still don’t know why) during the boost (one of the TPLs) configure step. This was difficult to track down, and I made the matter worse by symlinking gcc into /opt/homebrew/bin and /usr/local/bin, and then installing open-mpi. I cleaned my environment, clobbered /opt/homebrew and reinstalled homebrew, installed gfortran and openmpi.
Despite these efforts, the problem persisted until Ethan recommended removing an erroneously created symlink (MacOSX.sdk -> MacOSX13.3.sdk) in the SDKs folder. This solution resolved the Boost issue, enabling successful ATS installation.
For future MacOS installations, I plan to follow these steps before starting the bootstrap process:
- Install gfortran and open-mpi using Homebrew
- Verify gcc path (/usr/bin/gcc) and version (Apple clang)
- Check the gfortran path (/opt/homebrew/bin/gfortran)
- Confirm mpi and mpifort configurations (beginning with clang and gfortran, respectively; mpi -show)
Special thanks to Ethan, Konstantin, Fengming, and David for their guidance, and to everyone for their patience with the numerous emails.
Ethan Coon
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OLDHAM, GERALD
Do ATS have to be loaded on a Ubuntu server base or desktop (Ubuntu 23.04)?
From: ats-...@googlegroups.com <ats-...@googlegroups.com>
On Behalf Of Ethan Coon
Sent: Wednesday, November 15, 2023 7:12 AM
To: Rathore, Saubhagya <rath...@ornl.gov>
Cc: Coon, Ethan <coo...@ornl.gov>; Fengming Yuan <fmy...@gmail.com>; ats-...@googlegroups.com
Subject: Re: [EXTERNAL] Re: ATS installation error: Could NOT find BLAS (missing: BLAS_LIBRARIES)
I’m fairly confident that the underlying problem was multiple SDK installations (multiple versions of Xcode/commandline tools). If you upgrade a mac and see this problem, making sure to really clear out the old SDK before installing the new
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