Problem installing EGSnrc

[Rock-Jason]

Hi everyone!

I am having difficulty with my installation. Specifically, I am failing to complete the compilation of the EGSnrc c++ library.

I am using an M1 Mac, and trying to install egs using UTM (ubuntu). Installing on the Mac itself caused more problems, and I was able to get much farther this way.

The output from the configure script as well as the log are both attached. The compilers that I am using are also below.

Any help would be much appreciated!

configLog.txt
configOut.txt

`jasonrock@jason-mbp:/EGSnrc/HEN_HOUSE/log$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/11/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu122.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)

jasonrock@jason-mbp:/EGSnrc/HEN_HOUSE/log$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/11/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu122.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)

jasonrock@jason-mbp:/EGSnrc/HEN_HOUSE/log$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/11/lto-wrapper
Target: aarch64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu122.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu122.04)
jasonrock@jason-mbp:/
[EGSnrc/HEN_HOUSE/log$
`

[Rock-Jason]

Follow up, had issue formatting the compiler information. Apologies, see below:

jasonrock@jason-mbp:~/EGSnrc/HEN_HOUSE/log$ gcc -v Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/11/lto-wrapper Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu1~22.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04) jasonrock@jason-mbp:~/EGSnrc/HEN_HOUSE/log$ gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/11/lto-wrapper Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu1~22.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04) jasonrock@jason-mbp:~/EGSnrc/HEN_HOUSE/log$ g++ -v Using built-in specs. COLLECT_GCC=g++ COLLECT_LTO_WRAPPER=/usr/lib/gcc/aarch64-linux-gnu/11/lto-wrapper Target: aarch64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 11.4.0-1ubuntu1~22.04' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=aarch64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libquadmath --disable-libquadmath-support --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --enable-fix-cortex-a53-843419 --disable-werror --enable-checking=release --build=aarch64-linux-gnu --host=aarch64-linux-gnu --target=aarch64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04) jasonrock@jason-mbp:~/EGSnrc/HEN_HOUSE/log$

[mchamberland]

Just wondering if you tried installing on macOS using the instruction described in issue #1074? Specifically, the first step, that is to use the brew-installed gcc, which has a version number in its name, so as not to conflict with macOS gcc.

Also, did you migrate an older Mac to this M1 Mac or is it a fresh macOS install?

[Rock-Jason]

Hi, thanks for the help. I tried the suggestions for the #1074 thread on my native M1 Mac, yet I didn't make any further progress than before (it halts at compiling mortran3). This is why I moved to a linux installation, which no progress has been made too.

I am attaching a copy of the configure results, along with the log file
configure_copy.txt
configure.log

[crcrewso]

Try adding -std=f2003 to the fortan compile flags

So Input standard compilation flags: [-fPIC] would become
Input standard compilation flags: [-fPIC] -fPIC -std=f2003
In the log file there's references to features removed in the Fortran 2018 standard.

[Rock-Jason]

Hi, I seemed to solve the problem for M1 Mac (the linux problem is still unsolved, but I won't be pursuing it).

I had to make a new user on my Mac, and try the installation on the new user. The pre-dependencies (g++, gcc, etc) were already installed as \opt is higher up than \users in the system. During the EGSnrc installation, I did explicitly ask the compilers to use the specific versions (gcc-13, g++-13, etc), and it seemed to work!