JorgeRealP commented 2 years ago

Dear David Caress,

We’ve been trying to install nbsystem on a MacOS Monterey for several days during a campaign in the R/V Marcus G. Langseth. We managed to finish successfully all the pre-installation steps as indicated on the following page:

https://www.mbari.org/products/research-software/mb-system/how-to-download-and-install-mb-system/#toggle-id-7

However, when compiling the software (i.e., make install) systematically get the following problem:

Last 15 lines from /Users/jorge/Library/Logs/Homebrew/otps/01.make:

gfortran -o extract_HC -fconvert=swap -frecord-marker=4 extract_HC.f90 subs.f90 Undefined symbols for architecture x86_64: "gfortran_os_error_at", referenced from: _MAIN in ccyOwdGJ.o mapll in cc98kTT5.o mapxy in cc98kTT5.o _rd_modbody in cc98kTT5.o _rd_modbody1 in cc98kTT5.o ptide in cc98kTT5.o _writeuv in cc98kTT5.o ... ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make: *** [extract_HC] Error 1

that seem to have something to do with the compiler not able to recognize some “symbols”. We don’t know what else to do. Any hint would be very appreciated.

With best regards,

Jorge Real

dwcaress commented 2 years ago

Jorge,

Please move over to https://github.com/dwcaress/MB-System and post this issue there - Simon hasn't maintained his Homebrew MB-System installer in this repository for a long time. Or post to the MB-System discussion list at https://listserver.mbari.org/sympa/arc/mbsystem

What is the architecture of the machine - Intel or Arm (Apple Silicon)? If Intel then it is still possible to build a beta release MB-System using Homebrew. If it is an Arm machine then you will need to install the prerequisites using MacPorts rather than Homebrew.

Cheers, Dave

dwcaress commented 2 years ago

Here are some updated notes on installing the recent beta releases of MB-System that haven't made it to the web pages. This includes how to use MacPorts instead of Homebrew for the prerequisites.

-------------------------------------------------------------------------

Notes on using the MB-System autotools based build system

------------------------------------------------------------------------------

#

David W. Caress

May 12, 2022

------------------------------------------------------------------------------

#

This Autoconf build system was begun by Bob Covill in 2011, and then completed

with a distributed, multi-continental effort by Bob Covill, Christian

Ferreira, Hamish Bowman, Kurt Schwehr, and David Caress in May to August

of 2013.

#

------------------------------------------------------------------------------

To use the build system...

------------------------------------------------------------------------------

#

Obtain the MB-System source tree by either downloading and unpacking an

MB-System source distribution tarball (e.g. mbsystem-5.7.9.tar.gz) from

the Github repository:

https://github.com/dwcaress/MB-System/releases

#

To generate the makefiles needed to build MB-System, in a shell cd to the

top of the MB-System source tree and run ./configure with the options

appropriate for your situation. Some examples are given below.

#

After configure you can run the make utility in the usual fashion

make make install #

Some other useful make commands include:

make check (build and execute a limited set of unit tests) make clean (to delete compiled object files in the source code tree) make uninstall (to fully uninstall the installed libraries, headers, and programs) #

------------------------------------------------------------------------------

Configure script command line options:

------------------------------------------------------------------------------

Installation location:

------------------------

--prefix - This is the common installation prefix for all files.

If exec_prefix is defined to a different value, prefix

is used only for architecture-independent files.

[Default: /usr/local]

--exec_prefix - The installation prefix for architecture-dependent files.

By default it's the same as prefix. You should avoid

installing anything directly to exec_prefix. However,

the default value for directories containing

architecture-dependent files should be relative to

exec_prefix.

[Default: ${prefix} ==> /usr/local]

--datarootdir - The root of the directory tree for read-only architecture

-independent data files.

[Default: ${exec_prefix}/share ==> /usr/local/share]

--bindir - The directory for installing executables that users run.

[Default: ${exec_prefix}/bin ==> /usr/local/bin]

--libdir - The directory for installing object code libraries.

[Default: ${exec_prefix}/lib ==> /usr/local/lib]

--includedir - The directory for installing C header files.

[Default: ${exec_prefix}/include ==> /usr/local/include]

------------------------

MB-System configure options:

------------------------

--prefix=install - location for mbsystem (/usr/local/mbsystem) (optional)"])

--enable-hardening - Enable compiler and linker options to frustrate memory corruption exploits (e.g. -fPIE and -pie) (optional)"])

--enable-test - Enable building unit tests in test/ and third-party/"])

--with-netcdf-config - location of NetCDF config script nc-config (optional)"])

--with-gdal-config - location of GDAL config script gdal-config (optional)"])

--with-gmt-config - location of GMT config script gmt-config (optional)"])

--with-proj-lib - location of PROJ libs (optional)"])

--with-proj-include - location of PROJ headers (optional)"])

--with-fftw-lib - location of FFTW3 libs (optional)"])

--with-fftw-include - location of FFTW3 headers (optional)"])

--with-motif-lib - location of Motif libs (optional)"])

--with-motif-include - location of Motif headers (optional)"])

--with-opengl-lib - location of OpenGL libs (optional)"])

--with-opengl-include - location of OpenGL headers (optional)"])

--with-otps-dir - location of OTPS installation (optional)"])

--with-opencv-lib - location of OpenCV libs (optional)"])

--with-opencv-include - location of OpenCV headers (optional)"])

--enable-opencv - enable building tools using OpenCV (optional)"])

--enable-mbtrn - enable building terrain relative navigation (TRN) tools (optional)"])

--enable-mbtnav - enable building terrain relative navigation (TRN) tools (optional)"])

--disable-mbtools - disable building graphical tools (use with --enable-mbtrn and --enable-mbtnav)"])

--enable-qt - Enable building graphical tools using the Qt5 framework"])

--with-vtk-include - location of VTK8.2+ headers (required if qt enabled)"])

--with-vtk-lib - location of VTK8.2+ libraries (required if qt enabled)"])

--with-debug - Set compiler flags to allow full debugging"])

#

------------------------------------------------------------------------------

Setting X11 fonts used by mbgrdviz, mbeditviz, mbedit, mbnavedit, mbnavadjust

and mbvelocitytool:

------------------------------------------------------------------------------

By default the graphical utilities use three fonts: Helvetica, Times New

Roman, and Courier. This can be set in the CFLAGS environment variable by

including options of the form:

-DSANS='\"helvetica\"' -DSERIF='\"times\"' -DMONO='\"courier\"'

In the examples below, the CFLAGS environment value is set for the configure

script by setting it on the same command line as ./configure. To set the

fonts to Lucida, one might add:

-DSANS='\"lucida\"' -DSERIF='\"lucida\"' -DMONO='\"lucidatypewriter\"'

to the CFLAGS definition

#

------------------------------------------------------------------------------

MacOs Example Using MacPorts to Install Prerequisite packages:

------------------------------------------------------------------------------

#

The use of MacPorts to install the MB-System prerequisite packages is

recommended on Apple Mac computers, particularly because this approach enables

cleanly building with a complete X11 + Motif + OpenGL infrastructure separate

from the libraries and header files associated with the XQuartz package.

One usually still installs XQuartz and uses it as the X11 display server, but

confining the MB-System compiliation and linking to headers and libraries

within the MacPorts structure avoids several issues.

#

This example is relevant for MacOs 10.13 High Sierra to the current MacOs 12

Monterey on both Intel and ARM (Apple Silicon) architecture computers.

#

Install Xcode and the Xcode command line tools, which includes the LLVM

compiler suite.

#

Install the XQuartz X11 server from

https://www.xquartz.org

XQuartz 2.8 or later is required for MacOs Monterey and/or ARM architecture.

#

Install MacPorts using the appropriate downloadable installer package from:

https://www.macports.org/install.php

#

After MacPorts installation, first make sure the default port packages are

current by running selfupdate and then install the MB-System prerequisites.

sudo port -v selfupdate sudo port install gmt6 proj6 fftw-3 xorg mesa libGLU openmotif opencv4 #

Also make sure that a current version of Python3 is available. First list the

available Python3 versions, install the most recent, and then set port to link

that version to python3:

port select --list python sudo port install python310 port select --set python3 python310 #

Download the MB-System source package from the repository at GitHub:

https://github.com/dwcaress/MB-System

There are often beta releases that are more recent than the current stable

release. For instance, to download 5.7.9.beta29 go to:

https://github.com/dwcaress/MB-System/archive/refs/tags/5.7.9beta29.tar.gz

#

Unpack the MB-System distribution tarball, and then cd into the top directory

of the resulting structure. This will typically be named something like

"MB-System-5.7.9". At that location, execute the configure script, named

"configure", with the options necessary for your context. The XCode compiler

tools do not look for header files or libraries in the locations used by

MacPorts, and so it is necessary to specify these locations for several of

the prerequisite packages. #

This command should successfully enable building the current MB-System

(5.7.9 or later) on any Mac computer with the prerequisites installed through

MacPorts. This has been tested with computers running High Sierra through

Monterey. Note this command builds the core MB-System plus experimental

components including OpenCV based photomosaicing (enabled with

--enable-opencv) and a realtime Terrain Relative Navigation infrastructure

and toolset (--enable-mtrn and --enable-mbtnav).

./configure \
  --prefix=/usr/local \
  --disable-static \
  --enable-shared \
  --enable-hardening \
  --enable-test \
  --with-proj-lib=/opt/local/lib/proj6/lib \
  --with-proj-include=/opt/local/lib/proj6/include \
  --with-gmt-config=/opt/local/lib/gmt6/bin \
  --with-fftw-lib=/opt/local/lib \
  --with-fftw-include=/opt/local/include \
  --with-x11-lib=/opt/local/lib \
  --with-x11-include=/opt/local/include \
  --with-motif-lib=/opt/local/lib \
  --with-motif-include=/opt/local/include \
  --with-opengl-include=/opt/local/include \
  --with-opengl-lib=/opt/local/lib \
  --enable-mbtrn \
  --enable-mbtnav \
  --enable-opencv \
  --with-opencv-include=/opt/local/include/opencv4 \
  --with-opencv-lib=/opt/local/lib/opencv4 \
  --with-otps-dir=/usr/local/src/otps

#

Once the makefiles have been generated by configure, build and install

MB-System using:

    make
    make check
    sudo make install

#

------------------------------------------------------------------------------

MacOs Example Using Homebrew to Install Prerequisite packages:

------------------------------------------------------------------------------

#

The use of MacPorts to install the MB-System prerequisite packages is

recommended, but for Intel architecture computers and pre-Monterey OS versions

the use of Homebrew is still a viable option.

#

This example is relevant for MacOs Big Sur (11.6) on both Intel and ARM

architecture computers when the prerequisite software packages have been

installed using the Homebrew package manager. These commands will also

succeed in building MB-System on Macs running MacOs Monterey (11.7), but the

graphical programs will not execute properly on ARM Macs.

#

Install Xcode and the Xcode command line tools, which includes the LLVM

compiler suite.

#

Install the XQuartz X11 server from

https://www.xquartz.org (2.8 or later required for Monterey OS and/or ARM architecture)

#

Install the Homebrew package manager from https://brew.sh and then use brew

to install all of the the MB-System prerequisite packages:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

brew upgrade

brew install proj gdal netcdf fftw gmt openmotif

#

Unpack the MB-System distribution tarball, and then cd into the top directory

of the resulting structure. This will typically be named something like

MB-System-5.7.9/. At that location, execute the configure script, named "configure",

with the options necessary for your context. The XCode compiler tools do not

look for header files or libraries in the locations used by Homebrew, and so it

is necessary to specify these locations for several of the prerequisite packages.

On Intel architecture Macs, Homebrew installs packages into /usr/local/, while

on ARM architecture (Apple Silicon) Macs, Homebrew installs packages into

/opt/local/

#

In Intel Macs running Big Sur, the following command should succeed:

./configure \ --prefix=/usr/local \ --disable-static \ --enable-shared \ --enable-hardening \ --enable-test \ --with-x11-lib=/opt/X11/lib \ --with-x11-include=/opt/X11/include \ --with-motif-lib=/usr/local/opt/openmotif/lib \ --with-motif-include=/usr/local/opt/openmotif/include \ --with-opengl-include=/opt/X11/include \ --with-opengl-lib=/opt/X11/lib \ --with-otps-dir=/usr/local/src/otps #

In ARM Macs running Big Sur, the following command should succeed:

./configure \ --prefix=/usr/local \ --disable-static \ --enable-shared \ --enable-hardening \ --enable-test \ --with-x11-lib=/opt/X11/lib \ --with-x11-include=/opt/X11/include \ --with-opengl-lib=/opt/X11/lib \ --with-opengl-include=/opt/X11/include \ --with-motif-lib=/opt/homebrew/lib \ --with-motif-include=/opt/homebrew/include \ --with-otps-dir=/usr/local/src/otps #

Once the makefiles have been generated by configure, build and install

MB-System using:

    sudo make
    sudo make install

#

------------------------------------------------------------------------------

Ubuntu Linux configure script command line example:

------------------------------------------------------------------------------

#

The following procedure serves to install MB-System on Ubuntu Focal 20.04.

#

GMT:

----

GMT is a key prerequisite for MB-System, which now requires GMT 6.1 or later.

One can check which GMT version is available by querying the package manager in

a terminal:

    apt-cache show gmt

For Ubuntu 20.04 the available GMT version is 6.0.0. Therefore, it is necessary

to install GMT 6.1+ from a personal package archive (PPA) or by compiling,

linking, and installing the GMT source distribution manually.

#

One can enable installation from the UbuntuGIS PPA by entering the following

commands:

    sudo add-apt-repository ppa:ubuntugis/ppa
    sudo apt-get update
    sudo apt-get upgrade

#

Once GMT-6.1.0 or later is available to you, install the primary package and

the documentation, library files, development headers, and hierarchical high

resolution geography:

    sudo apt-get install gmt libgmt5 libgmt-dev gmt-gshhg gmt-doc

#

If you need (or want) to build GMT from source, follow the installation

instructions at:

https://www.generic-mapping-tools.org

#

Motif:

------

MB-System depends on X11, OpenMotif, and OpenGL. These can be installed using:

    sudo apt-get install libx11-dev xorg-dev libmotif-dev libmotif4 \
        libxp-dev mesa-common-dev libsdl1.2-dev libsdl-image1.2-dev

#

Other dependencies:

-------------------

The many other MB-System dependencies can be installed via:

    sudo apt-get install  build-essential gfortran nautilus-open-terminal \
        libfftw3-3 libfftw3-dev libnetcdf-dev netcdf-bin \
        libgdal-bin gdal-dev gv csh libgmt-dev libproj-dev

#

Everything at once:

-------------------

In fact, it should be possible to install all MB-System dependencies in a single

apt-get command:

    sudo apt-get install gmt libgmt5 libgmt-dev gmt-gshhg gmt-doc \
        libx11-dev xorg-dev libmotif-dev libmotif4 \
        libxp-dev mesa-common-dev libsdl1.2-dev libsdl-image1.2-dev \
        build-essential gfortran nautilus-open-terminal \
        libfftw3-3 libfftw3-dev libnetcdf-dev netcdf-bin \
        libgdal-bin gdal-dev gv csh libgmt-dev libproj-dev

#

MB-System:

----------

These steps assume you have downloaded an MB-System distribution tar.gz file

from the GitHub repository:

https://github.com/dwcaress/MB-System/releases

#

First, unpack the distribution using tar. This can be done in any location,

but if one is working in a root-owned area such as /usr/local/src, obtaining

root privileges using sudo is necessary for all steps:

sudo tar xvzf MB-System-5.7.9.tar.gz

and then cd into the resulting directory:

cd MB-System-5.7.9.tar.gz

#

If the prerequisites have all been installed as shown above, and it is desired

to install MB-System in /usr/local, then only a simple call to configure is

required:

   sudo ./configure

#

Once the makefiles have been generated by configure, build and install using:

    sudo make
    sudo make install

#

In some cases the system and/or user environment impedes the successful use of

the GMT and/or MB-System shared libraries. In order to manually allow shared

libraries to be found for linking or running, one can either set the CFLAGS

environment variable during building or set the LD_LIBRARY_PATH environment

variable at login by adding a command to the user's ~/.profile or ~/.bashrc files.

#

To set the CFLAGS environment variable during building include

"-Wl,-rpath -Wl,LIBDIR" in the configure command as shown here:

#

sudo CFLAGS="-Wl,-rpath -Wl,/usr/local/lib" ./configure

#

To augment the LD_LIBRARY_PATH environment variable during login add a line to

the ~/.bashrc or ~/.profile file as shown here:

#

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

# #

------------------------------------------------------------------------------

Completing the build and dealing with user environment issues

------------------------------------------------------------------------------

#

On all systems there are user environment setting that are required to use some

aspects of MB-System. First, three MB-System tools (mbswath, mbcontour, and

mbgrdtiff) are actually GMT modules built into a shared library named

"mbsystem.so". GMT only knows about these external modules through a user's

configuration, which is defined by a file called "gmt.conf" that is in

the user's home directory. To create this file, go to the home directory

and direct the output of the gmtdefaults module to a file named "gmt.conf":

    cd ~
    gmt gmtdefaults > gmt.conf

#

Next, use a text editor of your choice to edit the line of gmt.conf that

sets the "GMT_CUSTOM_LIBS" parameter so that this parameter is the full

path to the "mbsystem.so" shared library. If you have installed MB-System

in /usr/local, then the path should be "/usr/local/lib/mbsystem.so".

#

The MB-System plotting macros mbm_grdplot, mbm_plot, etc all generate

shellscripts that in turn execute a combination of GMT, MB-System, and other

programs to generate and then display postscript plots or images.

The MB-System program mbdefaults sets the programs you want to use to display

postscript files and images on the screen. If, for instance, you want to

use "gv" to display postscript and "feh" to display images, then run:

    mbdefaults -Dgv -Ifeh -V

These defaults are stored in a hidden file called ".mbio_defaults" in the user's

home directory.

------------------------------------------------------------------------------

dwcaress commented 2 years ago

And sorry about how that looks - Github is interpreting the notes as Markdown code when it is not...

JorgeRealP commented 2 years ago

David,

Thank you very much for the help. My computer is a 2015 mac with an intel processor. I am going to follow the steps that you recommend for the installation of the beta version for MBSYSTEM.

I apologize for opening this issue here (my first time using Github). The following I will put them where they should be.

Thanks

Jorge Real.

dwcaress commented 2 years ago

Jorge,

Since you have an old Intel Mac and already have Homebrew set up, first try:

brew tap dwcaress/mbsystem
brew install mbsystem-beta

I hope this helps.

Dave

On Jun 18, 2022, at 12:32 PM, JorgeRealP @.***> wrote:

David,

Thank you very much for the help. My computer is a 2015 mac with an intel processor. I am going to follow the steps that you recommend for the installation of the beta version for MBSYSTEM.

I apologize for opening this issue here (my first time using Github). The following I will put them where they should be.

Thanks

Jorge Real.

— Reply to this email directly, view it on GitHub https://github.com/zimonkaizoku/homebrew-mbsystem/issues/7#issuecomment-1159545295, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABTSXXH2TDJEGNOJK5LVUJLVPYP4PANCNFSM5ZEEUB5Q. You are receiving this because you commented.

David W. Caress Principal Engineer Seafloor Mapping Lab

Monterey Bay Aquarium Research Institute 7700 Sandholdt Road Moss Landing, CA 95039

@.*** http://www.mbari.org/~caress/

Phone: 831-775-1775

zimonkaizoku / homebrew-mbsystem

Help please. Can't install mbsystem #7

-------------------------------------------------------------------------

Notes on using the MB-System autotools based build system

------------------------------------------------------------------------------

David W. Caress

May 12, 2022

------------------------------------------------------------------------------

This Autoconf build system was begun by Bob Covill in 2011, and then completed

with a distributed, multi-continental effort by Bob Covill, Christian

Ferreira, Hamish Bowman, Kurt Schwehr, and David Caress in May to August

of 2013.

------------------------------------------------------------------------------

To use the build system...

------------------------------------------------------------------------------

Obtain the MB-System source tree by either downloading and unpacking an

MB-System source distribution tarball (e.g. mbsystem-5.7.9.tar.gz) from

the Github repository:

https://github.com/dwcaress/MB-System/releases

To generate the makefiles needed to build MB-System, in a shell cd to the

top of the MB-System source tree and run ./configure with the options

appropriate for your situation. Some examples are given below.

After configure you can run the make utility in the usual fashion

Some other useful make commands include:

------------------------------------------------------------------------------

Configure script command line options:

------------------------------------------------------------------------------

Installation location:

------------------------

--prefix - This is the common installation prefix for all files.

If exec_prefix is defined to a different value, prefix

is used only for architecture-independent files.

[Default: /usr/local]

--exec_prefix - The installation prefix for architecture-dependent files.

By default it's the same as prefix. You should avoid

installing anything directly to exec_prefix. However,

the default value for directories containing

architecture-dependent files should be relative to

exec_prefix.

[Default: ${prefix} ==> /usr/local]

--datarootdir - The root of the directory tree for read-only architecture

-independent data files.

[Default: ${exec_prefix}/share ==> /usr/local/share]

--bindir - The directory for installing executables that users run.

[Default: ${exec_prefix}/bin ==> /usr/local/bin]

--libdir - The directory for installing object code libraries.

[Default: ${exec_prefix}/lib ==> /usr/local/lib]

--includedir - The directory for installing C header files.

[Default: ${exec_prefix}/include ==> /usr/local/include]

------------------------

MB-System configure options:

------------------------

--prefix=install - location for mbsystem (/usr/local/mbsystem) (optional)"])

--enable-hardening - Enable compiler and linker options to frustrate memory corruption exploits (e.g. -fPIE and -pie) (optional)"])

--enable-test - Enable building unit tests in test/ and third-party/"])

--with-netcdf-config - location of NetCDF config script nc-config (optional)"])

--with-gdal-config - location of GDAL config script gdal-config (optional)"])

--with-gmt-config - location of GMT config script gmt-config (optional)"])

--with-proj-lib - location of PROJ libs (optional)"])

--with-proj-include - location of PROJ headers (optional)"])

--with-fftw-lib - location of FFTW3 libs (optional)"])

--with-fftw-include - location of FFTW3 headers (optional)"])

--with-motif-lib - location of Motif libs (optional)"])

--with-motif-include - location of Motif headers (optional)"])

--with-opengl-lib - location of OpenGL libs (optional)"])

--with-opengl-include - location of OpenGL headers (optional)"])

--with-otps-dir - location of OTPS installation (optional)"])

--with-opencv-lib - location of OpenCV libs (optional)"])

--with-opencv-include - location of OpenCV headers (optional)"])

--enable-opencv - enable building tools using OpenCV (optional)"])

--enable-mbtrn - enable building terrain relative navigation (TRN) tools (optional)"])

--enable-mbtnav - enable building terrain relative navigation (TRN) tools (optional)"])

--disable-mbtools - disable building graphical tools (use with --enable-mbtrn and --enable-mbtnav)"])

--enable-qt - Enable building graphical tools using the Qt5 framework"])

--with-vtk-include - location of VTK8.2+ headers (required if qt enabled)"])

--with-vtk-lib - location of VTK8.2+ libraries (required if qt enabled)"])

--with-debug - Set compiler flags to allow full debugging"])

------------------------------------------------------------------------------

Setting X11 fonts used by mbgrdviz, mbeditviz, mbedit, mbnavedit, mbnavadjust

and mbvelocitytool: