Problem while installing ROOT!

Esraa22 · July 27, 2022, 6:17pm

Hello !
Can anyone help me?
This error appeared while installing root. What should I do to avoid it?

[ 85%] Built target G__Rint
[ 85%] Built target Rint
[ 85%] Generating G__MathMore.cxx, ../../lib/MathMore.pcm
error: unable to open output file '/home/physicistesraa22/root_build/lib/MathMore.pcm': 'Operation not permitted'
In file included from input_line_10:7:
In file included from /home/physicistesraa22/root_build/include/Math/GSLMCIntegrator.h:38:
In file included from /home/physicistesraa22/root_build/include/Math/MCParameters.h:29:
/home/physicistesraa22/root_build/etc/cling/lib/clang/9.0.1/include/stddef.h:35:9: error: unknown type name '__PTRDIFF_TYPE__'
typedef __PTRDIFF_TYPE__ ptrdiff_t;
        ^
/home/physicistesraa22/root_build/etc/cling/lib/clang/9.0.1/include/stddef.h:46:9: error: unknown type name '__SIZE_TYPE__'
typedef __SIZE_TYPE__ size_t;
        ^
/home/physicistesraa22/root_build/etc/cling/lib/clang/9.0.1/include/stddef.h:60:9: error: unknown type name '__SIZE_TYPE__'
typedef __SIZE_TYPE__ rsize_t;
        ^
/home/physicistesraa22/root_build/etc/cling/lib/clang/9.0.1/include/stddef.h:74:9: error: unknown type name '__WCHAR_TYPE__'
typedef __WCHAR_TYPE__ wchar_t;
        ^
Error: /home/physicistesraa22/root_build/bin/rootcling: compilation failure (/home/physicistesraa22/root_build/lib/libMathMored1884d6f83_dictUmbrella.h)
make[2]: *** [math/mathmore/CMakeFiles/G__MathMore.dir/build.make:142: math/mathmore/G__MathMore.cxx] Error 1
make[1]: *** [CMakeFiles/Makefile2:26594: math/mathmore/CMakeFiles/G__MathMore.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

Wile_E_Coyote · July 27, 2022, 6:32pm

Exactly which ROOT version, which operating system version, which compiler version.

Esraa22 · July 27, 2022, 6:44pm

ROOT version is root_v6.26.04 on Ubuntu 22.04, but I am not sure about the compiler I only found the following>>>

physicistesraa22@ESRAA:~/root_build$ dpkg --list | grep compiler
ii  g++                                        4:11.2.0-1ubuntu1                       amd64        GNU C++ compiler
ii  g++-11                                     11.2.0-19ubuntu1                        amd64        GNU C++ compiler
ii  gcc                                        4:11.2.0-1ubuntu1                       amd64        GNU C compiler
ii  gcc-11                                     11.2.0-19ubuntu1                        amd64        GNU C compiler
ii  libllvm13:amd64                            1:13.0.1-2ubuntu2                       amd64        Modular compiler and toolchain technologies, runtime library
ii  libllvm14:amd64                            1:14.0.0-1ubuntu1                       amd64        Modular compiler and toolchain technologies, runtime library
ii  libxkbcommon0:amd64                        1.4.0-1                                 amd64        library interface to the XKB compiler - shared library
ii  llvm-14                                    1:14.0.0-1ubuntu1                       amd64        Modular compiler and toolchain technologies
ii  llvm-14-dev                                1:14.0.0-1ubuntu1                       amd64        Modular compiler and toolchain technologies, libraries and headers
ii  llvm-14-linker-tools                       1:14.0.0-1ubuntu1                       amd64        Modular compiler and toolchain technologies - Plugins
ii  llvm-14-runtime                            1:14.0.0-1ubuntu1                       amd64        Modular compiler and toolchain technologies, IR interpreter
ii  llvm-14-tools                              1:14.0.0-1ubuntu1                       amd64        Modular compiler and toolchain technologies, tools
ii  rpcsvc-proto                               1.4.2-0ubuntu6                          amd64        RPC protocol compiler and definitions

Wile_E_Coyote · July 27, 2022, 6:54pm

What was the CMake line that you used to configure it?

Esraa22 · July 27, 2022, 6:57pm

I used the installing from source then >>

cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src
cmake --build . -- install

Wile_E_Coyote · July 27, 2022, 7:04pm

Can it be that some disk is full? Try: df -h

Before trying to build your new ROOT, did you completely delete “~/root_src”, “~/root_build” and “~/root_install” directories (so that there is nothing that belongs to some old version)?

Esraa22 · July 27, 2022, 7:10pm

I tried de -h

physicistesraa22@ESRAA:~/root_build$  df -h
Filesystem      Size  Used Avail Use% Mounted on
tmpfs           337M  1.9M  335M   1% /run
/dev/sdb3        68G   20G   45G  30% /
tmpfs           1.7G     0  1.7G   0% /dev/shm
tmpfs           5.0M  4.0K  5.0M   1% /run/lock
/dev/sda1        96M   31M   66M  32% /boot/efi
tmpfs           337M  2.4M  335M   1% /run/user/1000
/dev/sdb5       228G  3.1G  225G   2% /media/physicistesraa22/01D8A116E32513C0
/dev/sda3       112G   50G   62G  45% /media/physicistesraa22/0A802A3F802A321D

No, I deleted nothing.
It stopped and I tried to resume it where it was but the errors also appeared.

Wile_E_Coyote · July 27, 2022, 7:18pm

I mean. You now try to build ROOT 6.26/04. If you had an older version (built previously), you should have deleted everything.

Esraa22 · July 27, 2022, 7:23pm

No, I haven’t any older versions, that’s the first time I install it.

Wile_E_Coyote · July 27, 2022, 7:28pm

So, it’s something for @Axel

BTW. The ROOT team provides ready-to-use binary distributions for some systems (see “Download a pre-compiled binary distribution” therein), including various Ubuntu versions, which you just need to download and unpack.
For Ubuntu 22.04 / x86_64 / gcc 11.2: https://root.cern/download/?C=M;O=A;P=*[uU][bB][uU][nN][tT][uU]*22*

Wile_E_Coyote · July 27, 2022, 8:38pm

Maybe one more check … do you have the “libgsl-dev” package installed?

Esraa22 · July 27, 2022, 8:48pm

Yes, it installed.
libgsl-dev/jammy,now 2.7.1+dfsg-3 amd64 [installed]

Axel · July 28, 2022, 9:34am

I am not sure I understand yet why you build ROOT yourself. It’s so much simpler to download the binaries as Wile_E proposed, or even use the binaries that conda offers. Please continue below only if you have a good reason to build ROOT rather than using pre-built binaries that just work.

Likely a permission problem; likely because you used sudo at some point (you shouldn’t). ls -l /home/physicistesraa22/root_build/lib/ should tell; or if the file already exists, ls -l /home/physicistesraa22/root_build/lib/MathMore.pcm.

You can fix the permissions using sudo chown -r physicistesraa22:physicistesraa22 /home/physicistesraa22/root_build/.

Esraa22 · July 28, 2022, 6:57pm

It works. But more errors appeared in XROOTD and VDT I don’t know why ? I really tried to solve them with no benefit.

Further more I installed conda and followed the steps of installing but it doesn’t work after some time the terminal window closes.
What I want to say is that I tried to install ROOT more than one time but no one succeeded. In every time, I face different errors and it is my first time so I am not familiar with using it.
Now, I want to clean all I did and start from the beginning with a successful way.
I will be grateful for help.
Thanks in advacne.

Axel · July 29, 2022, 3:53pm

It’s terrible to hear how difficult it is for you to install ROOT!

What operating system / distribution do you use - is this Ubuntu? Which version?

Conda should “just work”; it’s very surprising and a bug by itself if this doesn’t work. More details, please!

The problems you see with xrootd and vdt are what exactly? Would you be able to share the error messages?

Cheers, Axel

Esraa22 · July 29, 2022, 10:40pm

You’re right so, I’m little disappointed as I tried so many times. I can’t understand what is wrong I do?!

Yes, it is ubuntu22.04.
While installing through conda after creating the environment, the solving of the environment fails and retries again and then it ends with closing the terminal.
I followed these steps to install ROOT through Conda.

conda config --set channel_priority strict
conda create -c conda-forge --name ROOT root

The errors related to XROOTD and VDT; you can see in the attached photos because I deleted all I did and started again with installation through the main source. It is the only method that works with me.

Also an error appeared related to MathMore.The error is>

[ 87%] Generating G__MathMore.cxx, …/…/lib/MathMore.pcm
<<< cling interactive line includer >>>: fatal error: module file ‘/home/physicistesraa22/root_build/lib/Rint.pcm’ is out of date and needs to be rebuilt: could not read module signature
<<< cling interactive line includer >>>: note: imported by module ‘MathCore’ in ‘/home/physicistesraa22/root_build/lib/MathCore.pcm’
Error: Module ‘MathCore.pcm’ failed to load.
Error: Error loading the default rootcling header files.
make[2]: *** [math/mathmore/CMakeFiles/G__MathMore.dir/build.make:142: math/mathmore/G__MathMore.cxx] Error 1
make[1]: *** [CMakeFiles/Makefile2:26743: math/mathmore/CMakeFiles/G__MathMore.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

what should I do to continue installing correctly as this really consumes much time I need it.
Many thanks for you.

Axel · July 30, 2022, 5:45am

What about downloading https://root.cern/download/root_v6.26.06.Linux-ubuntu22-x86_64-gcc11.2.tar.gz and then just cd where-you-want-ROOT; tar xzf ~/Downloads/root_v6.26.06.Linux-ubuntu22-x86_64-gcc11.2.tar.gz?

Esraa22 · July 30, 2022, 2:41pm

I get the following>

physicistesraa22@ESRAA:~ mkdir root physicistesraa22@ESRAA:~ cd root/
physicistesraa22@ESRAA:~/root$ tar xzf ~/Downloads/root_v6.26.06.Linux-ubuntu22-x86_64-gcc11.2.tar.gz

gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

Esraa22 · July 30, 2022, 2:48pm

I want to continue installing from source, it reached 87% …
But what about the error I want to skip? How can I do that?
The error is above.

Wile_E_Coyote · July 30, 2022, 3:12pm

First, make sure you run: sudo apt-get install curl wget git

Then, assuming that “nproc” returns 4 or more and you have 8 GB RAM or more (if not, instead of “-j4” use “-j1”):