How does one turn the GDML feature ON during ROOT installation?

Hi,

I am having a hard time with GDMLs! I am trying to read a GDML file and it keeps saying error: use of undeclared identifier 'TGDMLParse'! I am not a GDML expert though, just trying to learn, and the file I am trying to read is perfectly OK.

This instruction says, we need to turn GDML option ON during config using ./configure --enable-gdml, but when I tried to do that ROOT complained about the deprecation of such a method and CMake must be used! Instructions seem outdated. Then I found this and tried cmake -DALL=ON ../root/, still didn’t get GDML working, then rebuilt ROOT using specifically cmake -DGDML=ON ../root/, did not work (ROOT installation went well though)! Getting the same error. (by the way, building from inside ROOT_BUILD directory and passing ../root/ as my source path) What am I missing here? By the way, here’s the complete error log:

Processing geoDisplay.C("../../gdml_files/activelar.gdml")...
Info in <TGeoManager::Import>: Reading geometry from file: ../../gdml_files/activelar.gdml
Info in <TGeoManager::TGeoManager>: Geometry GDMLImport, Geometry imported from GDML created
input_line_14:2:2: error: use of undeclared identifier 'TGDMLParse'
 TGDMLParse::StartGDML("../../gdml_files/activelar.gdml")
 ^
Error in <TGeoManager::Import>: Cannot open file
Error in <TGeoManager::CheckOverlaps>: Top node not set
Info in <TGeoManager::SetVisLevel>: Automatic visible depth disabled
#0  0x00007faf86c74687 in __GI___waitpid (pid=26689, stat_loc=stat_loc
entry=0x7ffc9ec6c608, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:30
#1  0x00007faf86bdf067 in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:149
#2  0x00007faf878125df in TUnixSystem::Exec (shellcmd=<optimized out>, this=0x561c7b10b740) at /.../root/core/unix/src/TUnixSystem.cxx:2118
#3  TUnixSystem::StackTrace (this=0x561c7b10b740) at /.../root/core/unix/src/TUnixSystem.cxx:2412
#4  0x00007faf82a10f05 in cling::MultiplexInterpreterCallbacks::PrintStackTrace() () from /.../ROOT_BUILD/lib/libCling.so       
#5  0x00007faf82a10998 in cling_runtime_internal_throwIfInvalidPointer () from /.../ROOT_BUILD/lib/libCling.so
#6  0x00007faf87f8f220 in ?? ()
#7  0x00007faf87f8f0c0 in ?? ()
#8  0x00007ffc9ec6e9d0 in ?? ()
#9  0x00007ffc9ec6ea60 in ?? ()
#10 0x00007ffc9ec6ea90 in ?? ()
#11 0x0000561c7b4fce70 in ?? ()
#12 0x00007ffc9ec6efb0 in ?? ()
#13 0x00007ffc9ec6e9f0 in ?? ()
#14 0x00007faf87f8f068 in ?? ()
#15 0x00007faf87af6300 in vtable for TString () from /.../ROOT_BUILD/lib/libCore.so
#16 0x0000005700000061 in ?? ()
#17 0x0000561c7c9bcdc0 in ?? ()
#18 0x00007faf87f8f000 in ?? ()
#19 0x00007ffc9ec6eab0 in ?? ()
#20 0x00007faf82a1146c in cling::Interpreter::RunFunction(clang::FunctionDecl const*, cling::Value*) [clone .part.268] () from /.../ROOT_BUILD/lib/libCling.so
#21 0x00007faf82a13c19 in cling::Interpreter::EvaluateInternal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, cling::CompilationOptions, cling::Value*, cling::Transaction**, unsigned long) () from /.../ROOT_BUILD/lib/libCling.so
#22 0x00007faf82ab1a0a in cling::MetaSema::actOnxCommand(llvm::StringRef, llvm::StringRef, cling::Value*) () from /.../ROOT_BUILD/lib/libCling.so
#23 0x00007faf82abdab7 in cling::MetaParser::isXCommand(cling::MetaSema::ActionResult&, cling::Value*) () from /.../ROOT_BUILD/lib/libCling.so
#24 0x00007faf82abeb96 in cling::MetaParser::isCommand(cling::MetaSema::ActionResult&, cling::Value*) () from /.../ROOT_BUILD/lib/libCling.so
#25 0x00007faf82aab529 in cling::MetaProcessor::process(char const*, cling::Interpreter::CompilationResult&, cling::Value*, bool) () from /.../ROOT_BUILD/lib/libCling.so
#26 0x00007faf82986f09 in HandleInterpreterException (metaProcessor=<optimized out>, input_line=<optimized out>, compRes=
0x7ffc9ec6efa4: cling::Interpreter::kSuccess, result=result
entry=0x7ffc9ec6efb0) at /.../root/core/metacling/src/TCling.cxx:1887
#27 0x00007faf82997da0 in TCling::ProcessLine (this=0x561c7b161690, line=<optimized out>, error=0x7ffc9ec700ec) at /.../metacling/src/TCling.cxx:2034
#28 0x00007faf82989b8d in TCling::ProcessLineSynch (this=0x561c7b161690, line=0x561c7ba313a0 ".X  /.../dunendggd/geoDisplay.C(\"../../gdml_files/activelar.gdml\")", error=0x7ffc9ec700ec) at /.../root/core/metacling/src/TCling.cxx:2886
#29 0x00007faf876f1bdc in TApplication::ExecuteFile (file=<optimized out>, error=0x7ffc9ec700ec, keep=<optimized out>) at /.../root/core/base/src/TApplication.cxx:1137
#30 0x00007faf876f3e3d in TApplication::ProcessLine (this=0x561c7b1576f0, line=<optimized out>, sync=<optimized out>, err=0x7ffc9ec700ec) at /.../root/core/base/src/TApplication.cxx:982
#31 0x00007faf87b556f2 in TRint::ProcessLineNr (this=this
entry=0x561c7b1576f0, filestem=filestem
entry=0x7faf87b673e4 "ROOT_cli_", line=line
entry=0x7ffc9ec700f0 ".x geoDisplay.C(\"../../gdml_files/activelar.gdml\")", error=error
entry=0x7ffc9ec700ec) at /.../root/core/rint/src/TRint.cxx:756
#32 0x00007faf87b56dc8 in TRint::Run (this=0x561c7b1576f0, retrn=<optimized out>) at /.../root/core/rint/src/TRint.cxx:416
#33 0x0000561c792fddfc in main (argc=<optimized out>, argv=0x7ffc9ec72278) at /.../root/main/src/rmain.cxx:30
Error in <HandleInterpreterException>: Trying to dereference null pointer or trying to call routine taking non-null arguments.
Execution of your code was aborted.
In file included from input_line_8:1:
/.../dunendggd/geoDisplay.C:12:2: warning: null passed to a callee that requires a non-null argument [-Wnonnull]
        geo->GetTopVolume()->Print();
        ^~~~~~~~~~~~~~~~~~~

[by the way, ROOT_BUILD is my $ROOTSYS, and /.../root/ is my source, but no idea why source directory will show up like this! I just have export ROOTSYS=/path/to/ROOT_BUILD.]

I also tried
root [0] gSystem->Load(libGdml) input_line_9:2:47: error: use of undeclared identifier 'libGdml' (((*(class TSystem **)0x7f892d2f9670))->Load(libGdml))
and I can’t find any gdmls here:

../../somewhere/~$ ls $ROOTSYS/lib | grep ml
libGuiHtml_rdict.pcm
libGuiHtml.rootmap
libGuiHtml.so
libHtml_rdict.pcm
libHtml.rootmap
libHtml.so

But inside my ROOT_BUILD, following are the only places I see any gdml inside my ROOT_BUILD:

/../ROOT_BUILD/etc/dictpch/geom/gdml
/../ROOT_BUILD/etc/dictpch/geom/gdml/inc
/../ROOT_BUILD/etc/dictpch/geom/gdml/inc/LinkDef.h

I would request you to update the instructions with an example, for example, this says

The command using the option `-D <var>:<type>=<value>` creates an entry in the CMake cache. This is the list of the ROOT specific CMake options:
There is a list of cmake variables given and a list of options, GDML, ALL, etc are listed under options, while things like CMAKE_INSTALL_PREFIX are listed under variables… what exactly one has to do to activate GDML or even ALL, one simple example would help a non-expert. So does this: cmake -DGDML=ON ../root/, make sense, what I did? If not, what should I do to make it work.

I would really appreciate any help.

Thank you


_ROOT Version: ROOT 6.10/04 [tags/v6-10-04@v6-10-04, May 04 2020, 07:22:00]
_Platform: Ubuntu 18.04.4 LTS
_Compiler: g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0


I also have GEANT4 [10.6.1], GeGeDe, DUNE GGD, CLHEP, etc installed on my Inspiron-5491-2n1.


cmake -Dall=ON ...
cmake -Dgdml=ON ...
gSystem->Load("libGdml")

The ROOT team provides ready-to-use binary distributions for some systems, including various Ubuntu versions, which you just need to download and unpack (see “Using binaries” therein).

2 Likes

I am facing a strange problem. I downloaded 6.20.04
wget https://root.cern/download/root_v6.20.04.Linux-ubuntu18-x86_64-gcc7.5.tar.gz
and unpacked it and changed my $ROOTSYS to this new directory, exported it… still the old version 6.10.04 opens each time I start root! echo $ROOTSYS returns the new path though! I even removed the old build (also $ROOTSYS) directory completely… the old version won’t go away! I removed the whole root directory, including the newly unpacked… everything is gone… still from somewhere the 6.20 opens up! How is this happening… Can you please help me completely purge ROOT out of my system so that I can start over.

What do you get from “which root” and “which root.exe

BTW. You should NOT manually set “ROOTSYS”. Follow the “Using binaries” instructions.

I get:

/usr/local/bin/root
/usr/local/bin/root.exe

@axel I’m not sure if there is any “uninstall” target now.

Previously, in the build directory, there could be an “install_manifest.txt” file which you could then use: xargs rm < install_manifest.txt

I also see:

~$ whereis root
root: /usr/local/bin/root.exe /usr/local/bin/root /usr/local/etc/root.desktop /usr/local/etc/root.mimes

should I just delete these files?

Following your answer from another thread:

sudo apt-get purge root-system* root-plugin* libroot*
 
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Package 'libroot-io-dev' is not installed, so not removed
Package 'libroot-io-xmlparser-dev' is not installed, so not removed
Package 'libroot-math-foam-dev' is not installed, so not removed
Package 'libroot-math-genvector-dev' is not installed, so not removed
Package 'libroot-math-mathcore-dev' is not installed, so not removed
Package 'libroot-math-mathmore-dev' is not installed, so not removed
Package 'libroot-math-matrix-dev' is not installed, so not removed
Package 'libroot-math-minuit-dev' is not installed, so not removed
Package 'libroot-math-mlp-dev' is not installed, so not removed
Package 'libroot-math-physics-dev' is not installed, so not removed
Package 'libroot-math-quadp-dev' is not installed, so not removed
Package 'libroot-math-smatrix-dev' is not installed, so not removed
Package 'libroot-math-splot-dev' is not installed, so not removed
Package 'libroot-math-unuran-dev' is not installed, so not removed
Package 'libroot-misc-memstat-dev' is not installed, so not removed
Package 'libroot-misc-minicern-dev' is not installed, so not removed
Package 'libroot-misc-table-dev' is not installed, so not removed
Package 'libroot-montecarlo-eg-dev' is not installed, so not removed
Package 'libroot-montecarlo-vmc-dev' is not installed, so not removed
Package 'libroot-net-auth-dev' is not installed, so not removed
Package 'libroot-net-bonjour-dev' is not installed, so not removed
Package 'libroot-net-dev' is not installed, so not removed
Package 'libroot-net-ldap-dev' is not installed, so not removed
Package 'libroot-proof-clarens-dev' is not installed, so not removed
Package 'libroot-proof-dev' is not installed, so not removed
Package 'libroot-proof-proofplayer-dev' is not installed, so not removed
Package 'libroot-roofit-dev' is not installed, so not removed
Package 'libroot-static' is not installed, so not removed
Package 'libroot-tmva-dev' is not installed, so not removed
Package 'libroot-tree-dev' is not installed, so not removed
Package 'libroot-tree-treeplayer-dev' is not installed, so not removed
0 upgraded, 0 newly installed, 0 to remove and 4 not upgraded.

Just removed /usr/local/bin/root and it was gone, unpacked binaries and everything is working well now. I can see GDML now :slight_smile:

Thanks!

install_manifest.txt should only be generated by make install.

I installed using make install, but I removed all root through rm -rf so probably lost that file! But, when whereis root returned /usr/local/bin, I removed them too and so got rid of all traces I guess. No I am using pre-compiled bianries as suggested by Wile_E_Coyote.

Post the output of:

/usr/local/bin/root-config --prefix
/usr/local/bin/root-config --exec-prefix
/usr/local/bin/root-config --bindir
/usr/local/bin/root-config --libdir
/usr/local/bin/root-config --incdir
/usr/local/bin/root-config --etcdir
/usr/local/bin/root-config --tutdir
/usr/local/bin/root-config --srcdir
/../acad$ /usr/local/bin/root-config --prefix; /usr/local/bin/root-config --exec-prefix; /usr/local/bin/root-config --bindir; /usr/local/bin/root-config --libdir; /usr/local/bin/root-config --incdir; /usr/local/bin/root-config --etcdir; /usr/local/bin/root-config --tutdir; /usr/local/bin/root-config --srcdir;
/usr/local
/usr/local
/usr/local/bin
/usr/local/lib
/usr/local/include
/usr/local/etc
Unknown argument "--tutdir"!
Usage: root-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] [--cflags] [--auxcflags] [--ldflags] [--new] [--nonew] [--libs] [--glibs] [--evelibs] [--bindir] [--libdir] [--incdir] [--etcdir] [--srcdir] [--noauxcflags] [--noauxlibs] [--noldflags] [--has-<feature>] [--arch] [--platform] [--config] [--features] [--ncpu] [--git-revision] [--python-version] [--cc] [--cxx] [--f77] [--ld ] [--help]
/../Software/acad/root

With the precompiled bianries, I am facing now this kind of problem. In my case the error is:

/from/somewhere/$ g++ -std=c++11  mycode.cpp `root-config --glibs --cflags` -o mycode
/../Software/acad/root/lib/libImt.so: undefined reference to `tbb::interface7::internal::isolate_within_arena(tbb::interface7::internal::delegate_base&, long)'
collect2: error: ld returned 1 exit status

Following this thread I changed LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib to LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATHand exported… but the error remains.

Two more:

/usr/local/bin/root-config --cflags
/usr/local/bin/root-config --libs

Here:

-pthread -std=c++11 -m64 -I/usr/local/include
-L/usr/local/lib -lCore -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lMultiProc -pthread -lm -ldl -rdynamic

So, you’ve got a real mess and I don’t have any easy solution.

Maybe @Axel can provide you with an appropriate full “install_manifest.txt” file for exactly the ROOT version that you built and installed (which you unfortunately deleted together with your “<builddir>”).

Otherwise, I think the only way would be to configure and build your original ROOT version (i.e. exactly the same version that you previously built and installed) from scratch again, using “cmake -Dall=ON ...”, and then execute “make install”. This will again create the “install_manifest.txt” file, which you can then use in order to remove all installed files: “sudo xargs rm < install_manifest.txt

I was actually doing that… right now make -j8 is at 73%… but of course some hundreds of lines of 73% … it will take a while…

I would like to see if this freshly made install (my original version) works OK… with GDML etc… then I am going to keep it… otherwise “ sudo xargs rm < install_manifest.txt ”.

But you do understand that the first answer to any problems will be … upgrade your ROOT version.

I actually have no idea how that happened! I install root through cmake and in other machines I have kept multiple versions and switch among them.

By the way, while make-ing this time, in the end… this happened:

[ 83%] Building CXX object hist/hist/CMakeFiles/Hist.dir/src/TPolyMarker.cxx.o
make[2]: *** No rule to make target '/acad/root/root_sources/root-v6-18-04/proof/proofx/src/TXSocketHandler.cxx', needed by 'proof/proofx/CMakeFiles/Proofx.dir/src/TXSocketHandler.cxx.o'.  Stop.
make[2]: *** Waiting for unfinished jobs....
Building CXX object proof/proofx/CMakeFiles/Proofx.dir/src/TXSocket.cxx.o
/bin/sh: 1: cd: can't cd to /acad/root/root_build/proof/proofx
proof/proofx/CMakeFiles/Proofx.dir/build.make:211: recipe for target 'proof/proofx/CMakeFiles/Proofx.dir/src/TXSocket.cxx.o' failed
make[2]: *** [proof/proofx/CMakeFiles/Proofx.dir/src/TXSocket.cxx.o] Error 2
make[2]: *** No rule to make target '/acad/root/root_sources/root-v6-18-04/hist/hist/src/TProfile2D.cxx', needed by 'hist/hist/CMakeFiles/Hist.dir/src/TProfile2D.cxx.o'.  Stop.
make[2]: *** Waiting for unfinished jobs....
Building CXX object hist/hist/CMakeFiles/Hist.dir/src/TPrincipal.cxx.o
/bin/sh: 1: cd: can't cd to /acad/root/root_build/hist/hist
hist/hist/CMakeFiles/Hist.dir/build.make:1529: recipe for target 'hist/hist/CMakeFiles/Hist.dir/src/TPrincipal.cxx.o' failed
make[2]: *** [hist/hist/CMakeFiles/Hist.dir/src/TPrincipal.cxx.o] Error 2
CMakeFiles/Makefile2:28879: recipe for target 'proof/proofx/CMakeFiles/Proofx.dir/all' failed
make[1]: *** [proof/proofx/CMakeFiles/Proofx.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
CMakeFiles/Makefile2:21836: recipe for target 'hist/hist/CMakeFiles/Hist.dir/all' failed
make[1]: *** [hist/hist/CMakeFiles/Hist.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

What Waiting for unfinished jobs it is talking about? My MySQL shell is open, could this be the reason? I was not doing anything else though… just importing some DB to my MySQL server and a shell was open.

Attaching the CMakeCache: CMakeCache_20-05-06_02-13-54.txt (156.3 KB)