Dear All,
I can confirm that I was able to compile and install Amber24
(including xLeap) using GCC14.1.0, by adding to
amber24_src/CMakeLists.txt:
set(CMAKE_C_FLAGS "-Wno-error=incompatible-pointer-types")
set(CMAKE_CXX_FLAGS "-Wno-error=incompatible-pointer-types")
I added those lines just after
set(INSIDE_AMBER TRUE).
However a few tests failed, raising floating point exceptions:
IEEE_UNDERFLOW_FLAG and IEEE_DENORMAL (see attached logs).
Regards,
Edwin.
El jue, 18 jul 2024 a las 21:31, Edwin Helbert Aponte Angarita
(<helbert2a.gmail.com>) escribió:
>
> Hi,
>
> I have removed amber24_src, extracted it again, updated and recompiled
> Amber24, this time ensuring that -DBUILD_GUI=FALSE was added. The
> compilation of the serial version was successful, however 7 tests
> failed (3 of them can be ignored). I attach the logs.
>
> When compiling the MPI version, I got incompatible pointer type errors again:
> /tmp/amber24_src/AmberTools/src/mdgx/Wrappers.c:121:18: error: passing
> argument 1 of ‘DefineMPITypes’ from incompatible pointer t
> ype [-Wincompatible-pointer-types]
> 121 | DefineMPITypes(&tj);
> | ^~~
> | |
> | trajcon ** {aka struct TrajectoryControlData
> **}
> In file included from
> /tmp/amber24_src/AmberTools/src/mdgx/Wrappers.c:9:
> /tmp/amber24_src/AmberTools/src/mdgx/MPITypeCast.h:6:30: note:
> expected ‘trajcon *’ {aka ‘struct TrajectoryControlData *’} but ar
> gument is of type ‘trajcon **’ {aka ‘struct TrajectoryControlData **’}
> 6 | void DefineMPITypes(trajcon *tj);
> | ~~~~~~~~~^~
> make[2]: *** [AmberTools/src/mdgx/CMakeFiles/libmdgx_mpi.dir/build.make:76:
> AmberTools/src/mdgx/CMakeFiles/libmdgx_mpi.dir/Wrappe
> rs.c.o] Error 1
> make[1]: *** [CMakeFiles/Makefile2:6636:
> AmberTools/src/mdgx/CMakeFiles/libmdgx_mpi.dir/all] Error 2
> make: *** [Makefile:156: all] Error 2
>
> Regards,
> Edwin.
>
> El jue, 18 jul 2024 a las 19:09, Edwin Helbert Aponte Angarita
> (<helbert2a.gmail.com>) escribió:
> >
> > Hi Timothy,
> >
> > Yes, as Scott pointed out previously, before cmake was made the build
> > system of Amber I could just have passed
> > AMBERBUILDFLAGS="-Wno-error=incompatible-pointer-types"
> > to make, but now that cmake is the build system, that can't be done.
> > Anyway, this error appears on some files
> > related to xLeap, so adding -DBUILD_GUI=FALSE in run_cmake should
> > allow me to compile it but without xLeap.
> > I thought that I had done that when I sent you my last email but after
> > double checking I realised that I hadn't. So I am
> > compiling it again at the moment (adding -DBUILD_GUI=FALSE in
> > run_cmake) and I will reply when that is done.
> >
> > Sorry about the confusion.
> >
> > I might also try adding
> >
> > set(CMAKE_C_FLAGS "Wno-error=incompatible-pointer-types")
> > set(CMAKE_CXX_FLAGS "Wno-error=incompatible-pointer-types")
> > to amber24_src/CMakeLists.txt.
> >
> > Regards,
> > Edwin.
> >
> > El jue, 18 jul 2024 a las 15:15, Timothy Giese
> > (<giese025.rutgers.edu>) escribió:
> > >
> > > The relevant portion of the log is:
> > >
> > > /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c:1108:49: error: passing argument 1 of ‘BuildRotateAroundBondFromTo’ from incompatible pointer type [-Wincompatible-pointer-types]
> > > 1108 | BuildRotateAroundBondFromTo( tTank->tank.uUnit,
> > > | ~~~~~~~~~~~^~~~~~
> > > | |
> > > | UNIT {aka UNITt *}
> > >
> > > From the developer-side, my guess is that this could possibly be fixed by including an explicit cast; e.g., (CONTAINER)(tTank->tank.uUnit). As a workaround, perhaps it could be built with -Wno-error=incompatible-pointer-types
> > > ________________________________
> > > From: Edwin Helbert Aponte Angarita via AMBER <amber.ambermd.org>
> > > Sent: Wednesday, July 17, 2024 9:31 PM
> > > To: Scott Brozell <sbrozell.comcast.net>; AMBER Mailing List <amber.ambermd.org>
> > > Subject: Re: [AMBER] Unable to compile Amber24 with gcc14.1.0
> > >
> > > Hi,
> > >
> > > Sorry for the late reply. I deleted amber24_src and followed the same
> > > procedure again. I attach the output of run_cmake (cmake.log) and
> > > make install (make_install_ser.log).
> > >
> > > OS: Slackware-current (rolling distro)
> > >
> > > gcc --version
> > > gcc (GCC) 14.1.0
> > >
> > > cmake --version
> > > cmake version 3.30.0
> > >
> > >
> > > Thanks,
> > > Edwin.
> > >
> > > On 7/13/24 2:30 AM, Scott Brozell wrote:
> > > > Hi,
> > > >
> > > > Wow, it really is like an episode of Gilligan's Island!
> > > > Apparently, the stdbool checking has gone awry.
> > > > Please send verbose and verbatim details:
> > > > OS name and version, gcc -v, cmake -version, your build/cmake.log file.
> > > > You can send the cmake.log directly to me since it is likely large.
> > > >
> > > > scott
> > > >
> > > > ps
> > > >
> > > > Amber: What's a funny quote from Gilligan's Island?
> > > > ChatTV: Professor: Well, that glue is permanent! There's nothing on the
> > > > island to dissolve it. Why do you know what it would take? It
> > > > would take a polyester derivative of an organic hydroxide molecule.
> > > >
> > > > Mr. Howell: Watch your language! You're in the presence of a chemist!
> > > >
> > > > On Fri, Jul 12, 2024 at 08:38:48PM +0100, Edwin Helbert Aponte Angarita via AMBER wrote:
> > > >> Thank you Scott for your reply. I tried with
> > > >> -DBUILD_GUI=FALSE
> > > >>
> > > >> and got different errors:
> > > >> [ 84%] Building C object AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/basics.c.o
> > > >>
> > > >> In file included from
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:41:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:385:9: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 385 | extern BOOL GbInterrupt;
> > > >> | ^~~~
> > > >>
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:450:8: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 450 | extern BOOL GbPrintPrefix;
> > > >>
> > > >> | ^~~~
> > > >>
> > > >> | sBOOL
> > > >>
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:779:8: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 779 | extern BOOL GbTestMemory;
> > > >>
> > > >> | ^~~~
> > > >>
> > > >> | sBOOL
> > > >>
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:962:8: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 962 | extern BOOL bStringToDouble( char *cPData,
> > > >> double *dPData );
> > > >> | ^~~~
> > > >>
> > > >> | sBOOL
> > > >>
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:963:8: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 963 | extern BOOL bStringToInt( char *cPData, int *iPData );
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:969:8: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 969 | extern BOOL bMessageCheck( char *sFile );
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:975:33:
> > > >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 975 | BOOL bComplain );
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> In file included from
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/zMatrix.h:43,
> > > >> from
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:43:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:83:46: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 83 | VECTOR *vPA, BOOL bA, VECTOR
> > > >> *vPB, BOOL bB,
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:83:68: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 83 | VECTOR *vPA, BOOL bA, VECTOR
> > > >> *vPB, BOOL bB,
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:84:46: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 84 | VECTOR *vPC, BOOL bC, VECTOR
> > > >> *vPD, BOOL bD );
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:84:68: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 84 | VECTOR *vPC, BOOL bC, VECTOR
> > > >> *vPD, BOOL bD );
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:57:1: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 57 | BOOL GbInterrupt = FALSE;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:237:1: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 237 | BOOL
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:261:1: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 261 | BOOL
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:317:1: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 317 | BOOL GbTestMemory = FALSE;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:347:42:
> > > >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 347 | DebugMemoryTest( char *sFile, int iLine, BOOL bReport )
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: In function
> > > >> ???DebugMalloc???:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:444:5: error:
> > > >> implicit declaration of function ???DebugMemoryTest???
> > > >> [-Wimplicit-function-declaration]
> > > >>
> > > >> 444 | DebugMemoryTest( sFile, iLine, FALSE );
> > > >> | ^~~~~~~~~~~~~~~
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: At top level:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:638:1: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 638 | BOOL
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:906:53:
> > > >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 906 | fBasicsMyFopen( char *sFilename, char *sAttributes, BOOL
> > > >> bComplain )
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:989:9: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 989 | BOOL bSinkUsed;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:990:9: error:
> > > >> unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 990 | BOOL bPrintPrefix;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: In function
> > > >> ???iCreatePrintSink???:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:1026:1:
> > > >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 1026 | BOOL bFoundOne;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: At top level:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:1198:1:
> > > >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 1198 | BOOL GbPrintPrefix = TRUE;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: In function
> > > >> ???myPrintString???:
> > > >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:1237:1:
> > > >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> > > >> 1237 | BOOL bPrintPrefix;
> > > >> | ^~~~
> > > >> | sBOOL
> > > >> make[2]: *** [AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/build.make:76: AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/basics.c.o]
> > > >> Error 1
> > > >>
> > > >> make[1]: *** [CMakeFiles/Makefile2:4993:
> > > >> AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/all]
> > > >> Error 2
> > > >> make: *** [Makefile:156: all] Error 2
> > > >>
> > > >>
> > > >> By the way, I knew about the difficulties to get inter-version
> > > >> portability with GNU compilers but not about the plight of the crew
> > > >> and passengers of SS Minnow. Good to learn something new.
> > > >>
> > > >> Regards,
> > > >> Edwin.
> > > >>
> > > >> On 7/12/24 1:52 PM, Scott Brozell wrote:
> > > >>> Hi,
> > > >>>
> > > >>> On Fri, Jul 12, 2024 at 01:34:34AM +0100, Edwin Helbert Aponte Angarita via AMBER wrote:
> > > >>>> I am trying to compile Amber24 using Gcc 14.1.0. I run:
> > > >>>> tar -xjf AmberTools24.tar.bz2
> > > >>>> tar -xjf Amber24.tar.bz2
> > > >>>> cd amber24_src
> > > >>>> ./update_amber --update
> > > >>>> cd build
> > > >>>> ./run_cmake
> > > >>>> make install
> > > >>>>
> > > >>>> and then I get the following error:
> > > >>>> [ 86%] Building C object AmberTools/src/leap/src/leap/CMakeFiles/leap_xleap_obj.dir/xAction.c.o
> > > >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c: In function
> > > >>>> ???zActionTwistTorsions???:
> > > >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c:1108:49:
> > > >>>> error: passing argument 1 of ???BuildRotateAroundBondFromTo??? from
> > > >>>> incompatible pointer type [-Wincompatible-pointer-types]
> > > >>>> 1108 | BuildRotateAroundBondFromTo( tTank->tank.uUnit,
> > > >>>> | ~~~~~~~~~~~^~~~~~
> > > >>>> | |
> > > >>>> | UNIT {aka UNITt *}
> > > >>>> In file included from
> > > >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c:52:
> > > >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/build.h:68:64: note:
> > > >>>> expected ???CONTAINER??? {aka ???struct CONTAINERSTRUCT *???} but
> > > >>>> argument is of type ???UNIT??? {aka ???UNITt *???}
> > > >>>
> > > >>> The latest version of GNU compilers used during release candidate
> > > >>> testing was 13.2.0. There are 2 ~easy workarounds:
> > > >>>
> > > >>> A. Install an older compiler; the latest from the 13 or 12 series are
> > > >>> likely to work. Then run clean_build and reinstall. This should
> > > >>> get you all of Amber.
> > > >>>
> > > >>> B. Edit run_cmake and add this to the appropriate cmake command:
> > > >>> -DBUILD_GUI=FALSE
> > > >>> Then rebuild. This should get you Amber without xLEaP.
> > > >>> If you need xLEaP, probably unlikely, then wait for us to
> > > >>> release a patch and then rebuild again.
> > > >>>
> > > >>> It'll likely be a few days before the patch becomes available.
> > > >>>
> > > >>>
> > > >>> In the dark ages, before cmake, users could've done this:
> > > >>> make AMBERBUILDFLAGS="-Wno-error=incompatible-pointer-types"
> > > >>>
> > > >>> Now that would've been an easy workaround.
> > > >>>
> > > >>>
> > > >>> It looks like there will be 5 of these errors across 3 files.
> > > >>> The patching should be straightforward, we just have to cast away
> > > >>> these 5 passengers from GNU's Island.
> > > >>>
> > > >>> Amber: What is GNU's Island ?
> > > >>> ChatTV: That's an allusion to the 1960's sitcom Gilligan's Island.
> > > >>>
> > > >>> Amber: Please elaborate.
> > > >>> ChatTV: I love your good manners!
> > > >>> Many episodes portray the passengers' and the crews' unsuccessful
> > > >>> attempts to escape their plight: Much like the application or
> > > >>> maintenance programmer is never able to escape the plight of the
> > > >>> ad hoc type-checking myopathy of the GNU compiler developers.
> > > >>>
> > > >>> Amber: Wow, that's deep!
> > > >>> ChatTV: Deep is as deep does.
> > > >>>
> > > >>> Amber: Do you think ?
> > > >>> ChatTV: I am.
> > > >>>
> > > >>> Amber: Ohh, Descartes!
> > > >>> ChatTV: No, that's a different TV show:
> > > >>> De plane! De plane!
> > > >>> from Fantasy Island.
> > > >>>
> > > >>> Amber: Say good night ChatTV.
> > > >>> ChatTV: Good night ChatTV!
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Received on Fri Jul 19 2024 - 11:30:02 PDT
