Re: [AMBER] amber16 Centos 7

From: Coleman, Marcus [JRDUS Non-J&J] <>
Date: Wed, 18 Jan 2017 03:08:57 +0000


I ran : "Make distclean" (started over)

Change to regular user and ran: "./configure -cuda gnu"

I am getting below error. Any suggestion would be greatly appreciated!

[mcolem19.f2 amber16]$ ./configure -cuda gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...

Available AmberTools 16 patches:

No patches available

Available Amber 16 patches:

No patches available

require development version of PythonCompatible Python found! Using
CUDA Version 8.0 detected
Configuring for SM2.0, SM3.0, SM5.0, SM5.2, SM5.3, SM6.0 and SM6.1

Obtaining the gnu compiler suite versions, e.g.:
     gcc -v
The C version is 4.8.5
The Fortran version is 4.8.5
./configure2: line 2254: testp.c: Permission denied

Testing the gcc compiler:
     gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
gcc: error: testp.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
./configure2: line 2266: ./testp: No such file or directory
Error: Unable to compile a C program using gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
       Please check your compiler settings or configure flags.
Configure failed due to the errors above!
[mcolem19.f2 amber16]$


[mcolem19.f2 amber16]$ whereis gcc
gcc: /usr/bin/gcc /usr/lib/gcc /usr/libexec/gcc /usr/share/man/man1/gcc.1.gz

[mcolem19.f2 amber16]$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO

[mcolem19.f2 amber16]$ which gcc
[mcolem19.f2 amber16]$

-----Original Message-----
From: Daniel Roe []
Sent: Tuesday, January 17, 2017 4:24 PM
To: AMBER Mailing List
Subject: [EXTERNAL] Re: [AMBER] amber16 Centos 7

We *strongly* recommend you do not install as root. It shouldn't be necessary and can potentially open the door to lots of problems.

As Hai suggested reading the Amber 16 manual section on Installation may be quite helpful. Another great resource is Jason Swail's wiki


On Tue, Jan 17, 2017 at 6:50 PM, Coleman, Marcus [JRDUS Non-J&J] <> wrote:
> From: Coleman, Marcus [JRDUS Non-J&J]
> Sent: Tuesday, January 17, 2017 3:47 PM
> To: ''
> Subject: Amber16 install Centos 7 missing amber 16 tools
> Hello
> I have install Amber 16 on Centos 7
> [root.f2 ~]# cat /etc/redhat-release
> CentOS Linux release 7.3.1611 (Core)
> [root.f2 ~]# uname -r
> 3.10.0-514.2.2.el7.x86_64
> [root.f2 ~]#
> [root.f2 amber16]# ./update_amber --update Preparing to apply
> updates... please wait.
> No new updates available for AmberTools 16 No new updates available
> for Amber 16
> Amber16 was previously install on an identical machine but not by me.
> The issue is /opt/amber16/bin directory is missings tons of files compared to the other identical machine.
> (see below)
> root.f2 ~]# cd /opt/amber16/bin
> [root.f2 bin]# pwd
> /opt/amber16/bin
> [root.f2 bin]# ls
> ######
> nc-config nccopy ncdump ncgen ncgen3 nf-config pmemd.cuda
> pmemd.cuda_DPFP pmemd.cuda_SPFP pmemd.cuda_SPXP ######
> [root.f2 bin]#
> [root.f1 ~]# cd /opt/amber16/bin
> [root.f1 bin]# pwd
> /opt/amber16/bin
> [root.f1 bin]# ls
> #####
> acdoctor fftw-wisdom-to-conf mmpbsa_py_energy
> addles fix_new_inpcrd_vel mmpbsa_py_nabnmode pmemd
> add_pdb frcmod2xml pmemd.cuda
> AddToBox func molsurf pmemd.cuda_DPFP sqm
> am1bcc gbnsr6 MTKppConstants pmemd.cuda_SPFP stats
> ambmask hcp_getpdb nab pmemd.cuda_SPXP stdLib2Sdf
> ambpdb hybrid nab2c prep2xml superimposer
> antechamber nc-config prepgen sviol
> lmanal nccopy process_mdout.perl sviol2
> atomtype makeANG_RST ncdump process_minout.perl teLeap
> bondtype makeCHIR_RST ncgen PropPDB tinker_to_amber
> capActiveSite makeDIST_RST ncgen3 protonator tleap
> match nef_to_RST pymdpbsa transform
> charmmgen match_atomname new2oldparm pytleap translate
> matextract new_crd_to_dyn reduce tss_init
> ChBox matgen new_to_old_crd residuegen tss_main
> CheckMD matmerge nf-config resp tss_next
> cphstats matmul nfe-umbrella-slice respgen ucpp
> MCPB nmode rism1d UnitCell
> cpptraj rism3d.orave volslice
> database mdgx paramfit rism3d.snglpnt xaLeap
> elsize mdnab parmcal rism3d.thermo xleap
> espgen parmchk sander xparmed
> parmchk2 sander.LES yacc
> fantasian minab parmed saxs_md
> mmE pbsa saxs_rism
> ffgbsa pdb4amber senergy
> fftw-wisdom pdbSearcher sequenceAligner
> #####
> [root.f1 bin]#
> How can I get all of the files listed above in /opt/amber16/ bin/...thanks..
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Tue Jan 17 2017 - 19:30:03 PST
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