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 Thu Jul 18 2024 - 14:00:01 PDT
