Hi,
I haven't ever been very successful using gcc 9.X to compile Amber.
Can you try upgrading to gcc 10?
-Dan
On Tue, Feb 28, 2023 at 5:07 PM Tang, Jun via AMBER <amber.ambermd.org> wrote:
>
> David,
>
> Thanks for looking into this issue,
>
> The build is in Ubuntu 18.04 with gcc 9.4.0 and nvcc 10.2.0. I use conda to install several packages (numpy scipy matplotlib setuptools cmake make cython swig fftw doxygen). Below are the run_cmake options I used
>
> cmake $AMBER_PREFIX/amber20_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber20 \
> -DCOMPILER=GNU \
> -DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=FALSE -DMINICONDA_USE_PY3=TRUE \
> 2>&1 | tee cmake.log
>
> I have already tried building from scratch a few times (with different compilers) and always hit the same error. Should I try again without using conda environment?
>
> Regards,
>
> Jun
>
> -----Original Message-----
> From: David A Case <david.case.rutgers.edu>
> Sent: Tuesday, February 28, 2023 3:27 PM
> To: Tang, Jun <juntangc.amazon.com>; AMBER Mailing List <amber.ambermd.org>
> Subject: RE: [EXTERNAL][AMBER] amber install error
>
> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you can confirm the sender and know the content is safe.
>
>
>
> On Tue, Feb 28, 2023, Tang, Jun via AMBER wrote:
>
> >I got an error while compiling ambermd. Please let me know how to get
> >around this error with "lvalue required as increment operand"
>
> Can you say what OS you are using? What options did you give to run_cmake?
>
> You seem to have most things in /home/ubuntu/src/ambermd/amber20_src, but there are also lots of references to /home/ubuntu/miniconda3, which suggests that you may have set that as your PYTHON_EXECUTABLE (?).
>
> >use_prebuilt_cythonized_files = False
>
> Not sure, but I'm a bit surprised at this message. We have seen this problem at least once before, but with no resolution (that I see). My general impression (from similar errors in other python projects) is that the cython extensions might have been made for a different version of python.
>
> It seems worth trying a fresh install with all defaults, if you've not already done that.
>
> ..good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 28 2023 - 16:30:02 PST
