Error building rosetta

[yipy0005]

Hi, I was running ./scons.py -j16 mode=release bin extras=mpi and everything was going well until scons: *** [build/external/release/linux/5.14/64/x86/gcc/11/mpi/libzlib.so] Error 127 happened. Could someone guide me on how to resolve it?

Thank you so much!

[dgront]

Personally I've never experienced such an error. A quick google search suggests that "a file can't be found". Kindly check if: - you have all executables on path - you have zlib library installed for the correct architecture. Is it 32/64 bits as the executable you are building? Is it in the devel version? is it on path? If this was not helpful, please provide more detailed error description to help you fixing it. Best, Dominik Gront wt., 13 sie 2024 o 13:20 Yip Yew Mun ***@***.***> napisał(a):

…

Hi, I was running ./scons.py -j16 mode=release bin extras=mpi and everything was going well until scons: *** [build/external/release/linux/5.14/64/x86/gcc/11/mpi/libzlib.so] Error 127 happened. Could someone guide me on how to resolve it? Thank you so much! — Reply to this email directly, view it on GitHub <#118>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAC3MI3XVYESEALHVSRA6HDZRHTYVAVCNFSM6AAAAABMOBUEN6VHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZXGA2DQNJQGE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[yipy0005]

Yes, I have the following paths:
gcc: /usr/bin/gcc
g++: /usr/bin/g++
openmpi: /usr/lib64/openmpi/bin & /usr/lib64/openmpi/lib/
Package zlib-1.2.11-40.el9.x86_64 is already installed.

Hope that helps. Please let me know if you need more info from me.

[dgront]

Hope that helps. Please let me know if you need more info from me.

Could you also paste the error message with context? wt., 13 sie 2024 o 14:12 Yip Yew Mun ***@***.***> napisał(a):

…

Yes, I have the following paths: gcc: /usr/bin/gcc g++: /usr/bin/g++ openmpi: /usr/lib64/openmpi/bin & /usr/lib64/openmpi/lib/ Package zlib-1.2.11-40.el9.x86_64 is already installed. Hope that helps. Please let me know if you need more info from me. — Reply to this email directly, view it on GitHub <#118 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAC3MI46FWHICGSFVEIMITDZRHZZ3AVCNFSM6AAAAABMOBUEN6VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMZSGUZDGOA> . You are receiving this because you commented.Message ID: ***@***.***>

[yipy0005]

error.log

./scons.py -j16 mode=release bin extras=mpi > error.log
sh: line 1: -L/usr/local/cuda-12.4/lib64${LD_LIBRARY_PATH -Lbuild/external/release/linux/5.14/64/x86/gcc/11/mpi/+ -Lexternal/+ -L/usr/lib64/openmpi/lib -Lbuild/external/release/linux/5.14/64/x86/gcc/11/mpi/}: bad substitution
sh: line 1: -L/usr/local/cuda-12.4/lib64${LD_LIBRARY_PATH -Lbuild/external/release/linux/5.14/64/x86/gcc/11/mpi/+ -Lexternal/+ -L/usr/lib64/openmpi/lib -Lbuild/external/release/linux/5.14/64/x86/gcc/11/mpi/}: bad substitution
scons: *** [build/external/release/linux/5.14/64/x86/gcc/11/mpi/libzlib.so] Error 127
scons: *** [build/external/release/linux/5.14/64/x86/gcc/11/mpi/libsqlite3.so] Error 127

[roccomoretti]

First off, your LD_LIBRARY_PATH setting in the Scons configuration is messed up. What's your source/tools/build/site.settings and/or source/tools/build/user.settings look like? I'd suggest using something like https://github.com/RosettaCommons/rosetta/blob/main/source/tools/build/site.settings.release

I'd also recommend first trying to build "plain", without extras=mpi and the associated build system changes. Even if you're not planning on using the non-MPI version, building MPI can be tricky, and doing it once without any MPI-related changes will help clarify what's MPI-related issues and what's general Rosetta build issues.

With the zlib issue, it may be that you have the "use" package, rather than the "devel" package. Is there a zlib-devel-1.2.11-40.el9.x86_64 or similar you can install?

[yipy0005]

Hi Rocco,

Here's my site.settings:

# -*- mode:python;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
#
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
# (c) addressed to University of Washington CoMotion, email: [email protected].

# These are settings for the topsail cluster at topsail.unc.edu.  It also works on kure.unc.edu.

# 3-11-09

# To use this file, symlink tools/build/site.settings to this file (or copy this file to that location)

# Settings here are added to the combined build settings, after all basic
# settings, to allow you to override anything you need to.  They can in turn
# be overriden by user settings and project settings respectively.
#
# Typically you want to prepend to one of the settings listed to expand your
# paths, but you can also append, override, or remove settings.

import os
settings = {
    "site" : {
                    "prepends" : {
            "program_path" : os.environ["PATH"].split(":"),
#            "include_path" : os.environ["INCLUDE"].split(":"),
            "library_path" : os.environ["LD_LIBRARY_PATH"].split(":"),
        },
        "appends" : {
        },
        "overrides" : {
        },
        "removes" : {
        },
    },
}

And my user.settings:

# -*- mode:python;indent-tabs-mode:nil;show-trailing-whitespace:t; -*-
#
# Copy this file into user.settings:
#
#   cp user.settings.template user.settings
#
# and customize to fit your site's environment
# DO NOT make changes to this template
# DO NOT try and check in user.settings
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
# (c) addressed to University of Washington CoMotion, email: [email protected].


# Settings here are added to the combined build settings, after all basic
# and site settings, to allow you to override anything you need to.
# They can in turn be overriden by the project settings.
#
# NOTE: At some point this file will allow you to have multiple settings
# and select between them from the options.  For now there is only the
# single "user" settings.

#import os
settings = {
    "user" : {
        "prepends" : {
        },
        "appends" : {
            # Uncomment the line below and the "import os" line above
            # to let SCons find ICC (assuming it's on your PATH already)
            # This is commented-out by default because it makes SCons
            # sensitive to your entire path.  This is necessary in
            # some environments, but has the unfortunate consequence
            # that any change whatsoever to the PATH variable (or its
            # contents) will force a complete recompile.
            #"program_path"  : os.environ["PATH"].split(":"),

            # Uncomment the line below to enable experimental mute level control in Tracer's
            #"defines" : [ 'EXPERIMENTAL_TRACER_FEATURES' ],
        },
        "overrides" : {
            ## Uncomment the following line to import the full operating system environment.  Useful for
            ## compiling with scons on different systems.
            #"ENV" : os.environ,
        },
        "removes" : {
        },
    }
}

And yes, my zlib packages are installed:

Installed Packages
zlib.x86_64                                                                                      1.2.11-40.el9                                                                                        @anaconda
zlib-devel.x86_64                                                                                1.2.11-40.el9                                                                                        @AppStream

Thanks for helping me with this, really appreciate it! 😄

[roccomoretti]

An issue might be your LD_LIBRARY_PATH settings in the environment. What does env | grep LD_LIBRARY_PATH (at the command line you're running scons from) print?

If you have the string LD_LIBRARY_PATH or curly braces on the right side of the equal sign, then you'll need to check your shell configuration files to make sure you're setting things appropriately.