Error in building O2 on new PC

O²
1

Dear all,

i was trying rebuilding O2Suite on macOS Monterey v12.6.1.
The command

aliBuild build O2Suite --defaults o2

fails at this step:

==> Building Python-modules-list@1.0
==> Python-modules-list is being built (use --debug for full output): failed
ERROR: Error while executing /Users/nicolanicassio/alice/sw/SPECS/osx_arm64/Python-modules-list/1.0-local1/build.sh on `MBP-DI-NICOLA.station’.
ERROR: Log can be found in /Users/nicolanicassio/alice/sw/BUILD/Python-modules-list-latest/log
ERROR: Please upload it to CERNBox/Dropbox if you intend to request support.
ERROR: Build directory is /Users/nicolanicassio/alice/sw/BUILD/Python-modules-list-latest/Python-modules-list.

This is the content of the log:

++ mkdir -p /Users/nicolanicassio/alice/sw/INSTALLROOT/4960e6218349f4e276ebaca51fbaeec8ebd6d65c/osx_arm64/Python-modules-list/1.0-local1/etc/modulefiles
++ alibuild-generate-module
BUILD_REQUIRES=alibuild-recipe-tools defaults-release
FULL_BUILD_REQUIRES=alibuild-recipe-tools defaults-release
DEFAULTS_RELEASE is a build_requires. Skipping loading the associated module.

I found previous posts on the error with Python-modules-list, but none of them worked.
Updating aliBuild as suggested in previous topics by other users did not work for me.

Do you have any idea on what could I do to solve this problem?

Thank you in advance,
Cheers,
Nicola

2

Hi,

Have you upgraded your system recently ? if so, have you updating the brew packages too ? (brew upgrade). Have you deleted your sw directory ?

I would start with that + run aliDoctor to check that everything is fine.

Cheers,
Barth

3

Hi, thanks for your answer.

The first thing i did yesterday was a fresh installation deleting sw.

This is what I did (in alice folder):

aliBuild init O2@dev --defaults o2
aliBuild init O2Physics@master --defaults o2
aliBuild init QualityControl@master --defaults o2
aliBuild build O2Suite --defaults o2

with the last comment giving the error.

No upgrade of the system was made with respect to some months ago were everything worked fine.

After I found this problem, reading on the forum here:

it was stated that someone solved this by updating aliBuild.

I did it by following the instructions for my OS and with the updated aliBuild I tried to install O2Suite (using the exact same command specified above, after deleting all folders in alice).

And i had the exact same problem at the exact same point.
Exactly after this I wrote here to ask for solutions.

This is the output have now with aliDoctor (using aliDoctor --defaults o2 O2Suite):

WARNING: Package golang cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING:
WARNING: REQUESTED_VERSION=1.22.2
WARNING: type go && case go version | sed -e 's/go version go//' | sed -e 's/ .*//' in 1.2[2-9].*) exit 0 ;; *) exit 1 ;; esac
WARNING:
WARNING: with the following output:
WARNING:
WARNING: golang: /bin/bash: line 1: type: go: not found
WARNING:
SUCCESS: Package CMake will be picked up from the system.
SUCCESS: Package libuv will be picked up from the system.
WARNING: Package FFTW3 cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING:
WARNING: REQUESTED_VERSION=v3.3.9
WARNING: false
WARNING:
WARNING: with the following output:
WARNING:
WARNING: FFTW3:
WARNING:
SUCCESS: Package lz4 will be picked up from the system.
SUCCESS: Package libpng will be picked up from the system.
SUCCESS: Package zlib will be picked up from the system.
WARNING: Package lzma cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING:
WARNING: REQUESTED_VERSION=v5.2.3
WARNING: printf “#include <lzma.h>\n” | c++ -xc++ - -c -M 2>&1
WARNING:
WARNING: with the following output:
WARNING:
WARNING: lzma: :1:10: fatal error: ‘lzma.h’ file not found
WARNING: lzma: #include <lzma.h>
WARNING: lzma: ^~~~~~~~
WARNING: lzma: 1 error generated.
WARNING:
SUCCESS: Package bz2 will be picked up from the system.
SUCCESS: Package Python will be picked up from the system.
SUCCESS: Package FreeType will be picked up from the system.
SUCCESS: Required package Python-system will be picked up from the system.
WARNING: Package hdf5 cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING:
WARNING: REQUESTED_VERSION=1.10.9
WARNING: printf “#include <hdf5.h>\n” | cc -xc - -c -o /dev/null
WARNING:
WARNING: with the following output:
WARNING:
WARNING: hdf5: :1:10: fatal error: ‘hdf5.h’ file not found
WARNING: hdf5: #include <hdf5.h>
WARNING: hdf5: ^~~~~~~~
WARNING: hdf5: 1 error generated.
WARNING:
SUCCESS: Required package rsync will be picked up from the system.
SUCCESS: Package GSL will be picked up from the system.
SUCCESS: Package libxml2 will be picked up from the system.
SUCCESS: Required package osx-system-openssl will be picked up from the system.
WARNING: Package TBB cannot be picked up from the system and will be built by aliBuild.
WARNING: This is due to the fact the following script fails:
WARNING:
WARNING: REQUESTED_VERSION=v2021.5.0
WARNING: printf “#include <tbb/concurrent_unordered_map.h>\n static_assert(TBB_INTERFACE_VERSION >= 11009, "min version check failed");\n” | c++ -std=c++11 -xc++ - -c -o /dev/null
WARNING:
WARNING: with the following output:
WARNING:
WARNING: TBB: :1:10: fatal error: ‘tbb/concurrent_unordered_map.h’ file not found
WARNING: TBB: #include <tbb/concurrent_unordered_map.h>
WARNING: TBB: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARNING: TBB: 1 error generated.
WARNING:
SUCCESS: Required package Xcode will be picked up from the system.
SUCCESS: Package xercesc will be picked up from the system.

==> The following packages will be built by aliBuild because
usage of a system version of it is not allowed or supported, by policy:

- Monitoring 
- flatbuffers 
- QualityControl 
- GMP 
- re2 
- Alice-GRID-Utils 
- FairRoot 
- Configuration 
- ZeroMQ 
- HepMC3 
- double-conversion 
- fastjet 
- MPFR 
- bookkeeping-api 
- libInfoLogger 
- Readout 
- XRootD 
- pythia 
- moderncppkafka 
- UUID 
- defaults-release 
- ms_gsl 
- Python-modules-list 
- simulation 
- lhapdf 
- GEANT4_VMC 
- coconut 
- FairMQ 
- Ppconsul 
- GEANT3 
- curl 
- xjalienfs 
- libwebsockets 
- protobuf 
- O2-customization 
- librdkafka 
- VecGeom 
- Common-O2 
- GEANT4 
- ITSResponse 
- xsimd 
- abseil 
- Control-Core 
- ONNXRuntime 
- vgm 
- GLFW 
- MLModels 
- cgal 
- AliEn-CAs 
- KFParticle 
- FairLogger 
- boost 
- pythia6 
- O2Physics 
- AliEn-Runtime 
- HepMC 
- utf8proc 
- libjalienO2 
- ninja 
- O2 
- FairCMakeModules 
- MCStepLogger 
- Vc 
- alibuild-recipe-tools 
- JAliEn-ROOT 
- generators 
- arrow 
- DebugGUI 
- CodingGuidelines 
- ROOT 
- fmt 
- O2Suite 
- Python-modules 
- googlebenchmark 
- RapidJSON 
- VMC 
- c-ares 
- grpc 
- json-c 
- ApMon-CPP 
- Control-OCCPlugin

==> The following packages will be picked up from the system:

- CMake
- libxml2
- xercesc
- FreeType
- Python
- zlib
- lz4
- libuv
- bz2
- GSL
- libpng

If this is not you want, you have to uninstall / unload them.

==> The following packages will be built by aliBuild because they couldn’t be picked up from the system:

- lzma
- hdf5
- TBB
- golang
- FFTW3

This is not a real issue, but it might take longer the first time you invoke aliBuild.
Look at the error messages above to get hints on what packages you need to install separately.