Hello
Thank you for your suggestion. You have mentioned to use AmberTools20
but I have the license for Amber16. How can I get Amber20?
I got the following error messages before "error: command 'gcc' failed
with exit status 1" line
pytraj/cyutils.cpp:19858:21: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
*type = tstate->exc_type;
^
pytraj/cyutils.cpp:19859:22: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
*value = tstate->exc_value;
^
pytraj/cyutils.cpp:19860:19: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
*tb = tstate->exc_traceback;
^
pytraj/cyutils.cpp: In function ‘void
__Pyx_ExceptionReset(PyObject*, PyObject*, PyObject*)’:
pytraj/cyutils.cpp:19872:24: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
tmp_type = tstate->exc_type;
^
pytraj/cyutils.cpp:19873:25: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
tmp_value = tstate->exc_value;
^
pytraj/cyutils.cpp:19874:22: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
tmp_tb = tstate->exc_traceback;
^
pytraj/cyutils.cpp:19875:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
tstate->exc_type = type;
^
pytraj/cyutils.cpp:19876:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
tstate->exc_value = value;
^
pytraj/cyutils.cpp:19877:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
tstate->exc_traceback = tb;
^
pytraj/cyutils.cpp: In function ‘int __Pyx_GetException(PyObject**,
PyObject**, PyObject**)’:
pytraj/cyutils.cpp:19920:24: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
tmp_type = tstate->exc_type;
^
pytraj/cyutils.cpp:19921:25: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
tmp_value = tstate->exc_value;
^
pytraj/cyutils.cpp:19922:22: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
tmp_tb = tstate->exc_traceback;
^
pytraj/cyutils.cpp:19923:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
tstate->exc_type = local_type;
^
pytraj/cyutils.cpp:19924:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
tstate->exc_value = local_value;
^
pytraj/cyutils.cpp:19925:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
tstate->exc_traceback = local_tb;
^
pytraj/cyutils.cpp: In function ‘void
__Pyx_ExceptionSwap(PyObject**, PyObject**, PyObject**)’:
pytraj/cyutils.cpp:21572:24: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
tmp_type = tstate->exc_type;
^
pytraj/cyutils.cpp:21573:25: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
tmp_value = tstate->exc_value;
^
pytraj/cyutils.cpp:21574:22: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
tmp_tb = tstate->exc_traceback;
^
pytraj/cyutils.cpp:21575:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_type’
tstate->exc_type = *type;
^
pytraj/cyutils.cpp:21576:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_value’
tstate->exc_value = *value;
^
pytraj/cyutils.cpp:21577:13: error: ‘PyThreadState {aka struct _ts}’
has no member named ‘exc_traceback’
tstate->exc_traceback = *tb;
Thank you.
----- Message from David A Case <david.case.rutgers.edu> ---------
Date: Thu, 21 Jan 2021 08:16:12 -0500
From: David A Case <david.case.rutgers.edu>
Reply-To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Fwd: Error during amber16 installation
To: AMBER Mailing List <amber.ambermd.org>
> On Thu, Jan 21, 2021, spss4.iacs.res.in wrote:
>> I am trying to install Amber16 in ubuntu16.04 system according to the steps
>> described in the manual. I am getting the following error during make
>> install
>>
>> error: command 'gcc' failed with exit status 1
>> Makefile:456: recipe for target 'pytraj' failed
>
> You should capture the output of the make command, e.g.
>
> make install | tee make.errors
>
> Then look for the relevant error messages in the "make.errors" file. You
> will want to look at what happens right before the "gcc failed" line.
>
> Better: download AmberTools20 and try that. It may no longer be possible
> to install pytraj on an raw AmberTools16 installation, since there have been
> changes in various python components since then. You'll want to use
> AmberTools20 in any event, even if you continue to use pmemd from Amber16.
> But consider upgrading to Amber20 as well.
>
> ...good luck....dac
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.orghttps://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=euGZstcaTDllvimEN8b7jXrwqOf-v5A_CdpgnVfiiMM&r=8kcPn14zQtytNPxPVfnim16FaKEi4wCg1Z7tzwtgsBc&m=WyOEvK8KkOWWQwbI7eVMUKClbKcx2Ak5GuBjkcbHO08&s=nqxPrCVpk0MvEQRGwEvD3J6x99hxUK86xBzVPrTGeD4&e=
----- End message from David A Case <david.case.rutgers.edu> -----
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Received on Thu Jan 21 2021 - 21:00:02 PST
