Re: [AMBER] amber install error

From: Tang, Jun via AMBER <>
Date: Tue, 28 Feb 2023 21:40:07 +0000


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 \
    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?



-----Original Message-----
From: David A Case <>
Sent: Tuesday, February 28, 2023 3:27 PM
To: Tang, Jun <>; AMBER Mailing List <>
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

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Received on Tue Feb 28 2023 - 14:30:02 PST
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