VMD-L Mailing List

From: Chris Taylor (christay_at_usc.edu)
Date: Thu Jan 07 2021 - 17:25:09 CST

Here’s what I did- I’m following the installation instructions in the programmer’s manual, but I don’t think I missed anything (maybe I did).

I cd’d into the source directory and added this to the configure.options:

[ec2-user_at_ip-172 vmd-1.9.4a51]$ cat configure.options
LINUX MESA FLTK TK ACTC MPI LIBOSPRAY TCL PTHREADS SILENT
[ec2-user_at_ip-172-31-18-188 vmd-1.9.4a51]$ ./configure
using configure.options: LINUX MESA FLTK TK ACTC MPI LIBOSPRAY TCL PTHREADS SILENT

Then I followed the steps in the install guide to make the source like this:
[ec2-user_at_ip-172 vmd-1.9.4a51]$ cd src
[ec2-user_at_ip-172 src]$ make veryclean
[ec2-user_at_ip-172 src]$ make
Compiling OpenGLDisplayDevice.C --> OpenGLDisplayDevice.o ...
In file included from /usr/include/features.h:447:0,
                 from /usr/include/c++/7/x86_64-redhat-linux/32/bits/os_defines.h:39,
                 from /usr/include/c++/7/x86_64-redhat-linux/32/bits/c++config.h:533,
                 from /usr/include/c++/7/cstdlib:41,
                 from /usr/include/c++/7/stdlib.h:36,
                 from OpenGLDisplayDevice.C:24:
/usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file or directory
# include <gnu/stubs-32.h>
           ^~~~~~~~~~~~~~~~
compilation terminated.
make: *** [OpenGLDisplayDevice.o] Error 1

From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Thursday, January 7, 2021 15:14
To: Chris Taylor <christay_at_usc.edu>
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: RE: Install VMD from source on Amazon EC2 instance

On Thu, Jan 7, 2021 at 6:10 PM Chris Taylor <christay_at_usc.edu<mailto:christay_at_usc.edu>> wrote:
Also, just to be clear I want to build a 64-bit version of VMD. It’s just that it seems like it wants to build some part of it using a 32-bit library, but I’m not sure why.

that makes no sense. as already requested, please provide more information about the individual steps you did and how you configured VMD to be compiled from source.

axel.

Chris

From: Chris Taylor
Sent: Thursday, January 7, 2021 14:54
To: Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: RE: vmd-l: RE: Install VMD from source on Amazon EC2 instance

I get this error when I try to compile, and when I looked it up it seems to point to the lack of a package like glibc-devel.i686 – the 32bit development libs for this version of Linux. The information I’ve found online is that Amazon makes 32bit runtime libraries available in their version of Linux but not the development libraries. I think it would be nice to be able to run VMD on an AWS Amazon Linux2 VM, because I’ve been doing some work with their ParallelCluster and it would be cool to run an MPI version of VMD.

/usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file or directory
# include <gnu/stubs-32.h>
           ^~~~~~~~~~~~~~~~
compilation terminated.
make: *** [OpenGLDisplayDevice.o] Error 1

From: Axel Kohlmeyer <akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>>
Sent: Thursday, January 7, 2021 14:49
To: Chris Taylor <christay_at_usc.edu<mailto:christay_at_usc.edu>>
Cc: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: RE: Install VMD from source on Amazon EC2 instance

why are you trying to build 32-bit binaries in the first place since you appear to be running on a 64-bit host?
you need to provide more information about what it is exactly that you were doing for people to be able to give meaningful advice.

axel.

On Thu, Jan 7, 2021 at 5:34 PM Chris Taylor <christay_at_usc.edu<mailto:christay_at_usc.edu>> wrote:
Just wondering if anybody had any ideas for me on this? Maybe there’s a compiler directive or option I can give to work around it? Thanks
Chris

From: Chris Taylor
Sent: Monday, January 4, 2021 16:54
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>
Subject: RE: Install VMD from source on Amazon EC2 instance

I get this error when I try to ‘make’ vmd-1.9.4a51. This is on a Amazon Linux2 EC2 instance, and they seem to be saying I can’t download something like glibc6-devel.i686 or whatever it is to give me the 32-bit build dependencies- they don’t provide those RPMs. I want to try to build from source because I want to compile MPI in. Under the circumstances, what are my options? Thanks.

$ make
Compiling OpenGLDisplayDevice.C --> OpenGLDisplayDevice.o ...
In file included from /usr/include/features.h:447:0,
                 from /usr/include/c++/7/x86_64-redhat-linux/32/bits/os_defines.h:39,
                 from /usr/include/c++/7/x86_64-redhat-linux/32/bits/c++config.h:533,
                 from /usr/include/c++/7/cstdlib:41,
                 from /usr/include/c++/7/stdlib.h:36,
                 from OpenGLDisplayDevice.C:24:
/usr/include/gnu/stubs.h:7:11: fatal error: gnu/stubs-32.h: No such file or directory
# include <gnu/stubs-32.h>
           ^~~~~~~~~~~~~~~~
compilation terminated.
make: *** [OpenGLDisplayDevice.o] Error 1 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!oJJOf5J-mXYgDhDJhCO-d1B-oNv-rUy8TPmd_1bA_KqnRZmFPfzEmWUOcWfDRSNHUw$ <https://urldefense.com/v3/__http:/goo.gl/1wk0__;!!LIr3w8kk_Xxm!9UZPqf4wCjBs61AbQsteLIZacQY4OZUb-Uj3-jtof3T1JFF0LsmfhsRbyDpj3b0$>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.
--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!oJJOf5J-mXYgDhDJhCO-d1B-oNv-rUy8TPmd_1bA_KqnRZmFPfzEmWUOcWfDRSNHUw$ <https://urldefense.com/v3/__http:/goo.gl/1wk0__;!!LIr3w8kk_Xxm!5Y5WzptQ1HkJjJRBnxlirQbZqZdebbl0Yd3JGWrRbBY0lmkpZdAKFx20VGnOzuU$>
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.