From owner-chemistry@ccl.net Tue Oct 1 01:55:01 2013 From: "Van Dam, Hubertus J HubertusJJ.vanDam],[pnnl.gov" To: CCL Subject: CCL: Compiling nwchem-6.3 in redhat linux Message-Id: <-49213-131001014831-10074-/XeYFym9AjsF9J61hPrS8A:+:server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_FDD09CBD8676AE40957DCDAD24E9627A0191E9EE5E19EMAIL04pnlg_" Date: Mon, 30 Sep 2013 22:48:15 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam]*[pnnl.gov] --_000_FDD09CBD8676AE40957DCDAD24E9627A0191E9EE5E19EMAIL04pnlg_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Shilpi, I think you have essentially two options: 1. You can do the compilation along the lines you tried initially, ho= wever in that case I would recommend to have the environment variable NWCHE= M_MODULES defined before issuing "make nwchem_config". Also I would recomme= nd specifying the compilers you want to use on the make line, e.g. "make FC= =3Dgfortran CC=3Dgcc". Please do not specify the MPI compiler wrappers as c= ompilers as the make procedure uses the actual compiler names to establish = what flags the compiler understands. 2. You try the ./contrib/distro-tools/build_nwchem script. However, t= his script has been designed to try and establish as much as it can by itse= lf. You should only have to set the things that the script guesses wrong (o= therwise you override what the script thinks it should be doing and that ca= n confuse things badly). In short the script requires only that mpif90, mpi= cc and mpiCC are in your path. The script will query these commands to figu= re out things like what the MPI libraries are, where the MPI include files = live, etc. Setting BLASOPT=3D" " is a good idea though if you want NWChem t= o compile with the internal BLAS and LAPACK libraries rather than trying to= find some of those on your machine. Some more information can be found at:= http://www.nwchem-sw.org/index.php/Compiling_NWChem#How-to:_Build_nwchem_s= cript (this page also contains more details on other mechanisms to build NW= Chem). If you still get stuck, please let me know. Huub van Dam Pacific Northwest National Laboratory Tel: 509-372-6441 > From: owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov()ccl.net [mailto:owner-c= hemistry+hubertus.vandam=3D=3Dpnnl.gov()ccl.net] On Behalf Of Marcel Swart m= arcel.swart^^^icrea.cat Sent: Saturday, September 28, 2013 1:55 PM To: Van Dam, Hubertus J Subject: CCL: Compiling nwchem-6.3 in redhat linux You could try with: export LARGE_FILES=3Dtrue export NWCHEM_TOP=3D/home/user1/nwchem export NWCHEM_TARGET=3DLINUX64 export NWCHEM_MODULES=3D"smallqm" export FC=3Dmpif90 export CC=3Dmpicc export USE_MPI=3D"y" export MPI_LOC=3D$OMPI export MPI_LIB=3D$MPI_LOC/lib64 export MPI_INCLUDE=3D$MPI_LOC/include export BLASOPT=3D" " cd $NWCHEM_TOP ./contrib/distro-tools/build_nwchem On 28 Sep 2013, at 18:41, John Keller jwkeller^alaska.edu > wrote: Dear Shilpi, This request should go to the NWChem community/compiling users forum. The N= WChem developers answer compile questions directly on that forum. http://www.nwchem-sw.org/index.php/Special:AWCforum John Keller University of Alaska Fairbanks On Sat, Sep 28, 2013 at 3:23 AM, Shilpi V shilpigre-*-gmail.com > wrote= : Sent to CCL by: "Shilpi V" [shilpigre---gmail.com] Dear all, I have tried installing Nwchem-6.3 following the instructions given in the = INSTALL file. I did the following steps make -v export LARGE_FILES TRUE export USE_NOFSCHECK TRUE export TCGRSH=3D/usr/local/bin/ssh export NWCHEM_TOP=3D/home/user1/nwchem export NWCHEM_TARGET LINUX64 cd $NWCHEM_TOP/src make nwchem_config NWCHEM_MODULES=3Dpnnl make >& make.log Here, the make.log gives the following, config/makefile.h:145: /home/user1/nwchem/-6.3/src/config/nwchem_config.h: = No such file or directory ----- You must set NWCHEM_MODULES to the list of modules to be included in NWChem= builds. The following modules are known: NWints atomscf ddscf develop gradients moints nwdft nwxc rimp2 stepper driv= er optim scfaux cphf ccsd vib mcscf prepar esp hessian plane_wave selci dpl= ot mp2_grad oimp2 qhop property nwpw fft rimp2_grad python argos analyz dia= na nwmd cafe space drdy vscf uccsdt qmmm rism qmd etrans tce geninterface b= q cons perfm dntmc transport smd nbo dangchang leps ccca The following shorthand names are also recognized: all qm md classical tps alldev pnnl pnnldev smallqm You must define NWCHEM_TARGET in your environment to be the name of the machine you wish to build for ... for example setenv NWCHEM_TARGET SOLARIS Known targets are SOLARIS, SGI_N32, ... See the INSTALL instructions for a complete list make: *** [error2] Error 2 Please, make me get rid of this error and install Nwchem successfully. Thank You, V. Shilpi -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY#,#ccl.net or u= se:E-mail to administrators: CHEMISTRY-REQUEST#,#ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml marcel.swart-.-udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --_000_FDD09CBD8676AE40957DCDAD24E9627A0191E9EE5E19EMAIL04pnlg_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Shilpi,

 

I think you have essentially two options:

1= .     = ;  You can do the compilation al= ong the lines you tried initially, however in that case I would recommend t= o have the environment variable NWCHEM_MODULES defined before issuing ̶= 0;make nwchem_config”. Also I would recommend specifying the compiler= s you want to use on the make line, e.g. “make FC=3Dgfortran CC=3Dgcc= ”. Please do not specify the MPI compiler wrappers as compilers as th= e make procedure uses the actual compiler names to establish what flags the= compiler understands.

2.       = You try the ./contrib/distro-tools/build_nwchem script. However, thi= s script has been designed to try and establish as much as it can by itself= . You should only have to set the things that the script guesses wrong (oth= erwise you override what the script thinks it should be doing and that can = confuse things badly). In short the script requires only that mpif90, mpicc= and mpiCC are in your path. The script will query these commands to figure= out things like what the MPI libraries are, where the MPI include files li= ve, etc. Setting BLASOPT=3D” “ is a good idea though if you wan= t NWChem to compile with the internal BLAS and LAPACK libraries rather than= trying to find some of those on your machine. Some more information can be= found at: http://www.nwchem-sw.org/index.php/Compiling_NW= Chem#How-to:_Build_nwchem_script (this page also contains more details = on other mechanisms to build NWChem).

If you still get stuck, please let me know.

 

Huub van Dam
Pacific Northwest National Labor= atory
Tel:  509-372-6441


 

From: owner-chem= istry+hubertus.vandam=3D=3Dpnnl.gov()ccl.net [mailto:owner-chemistry+hubertu= s.vandam=3D=3Dpnnl.gov()ccl.net] On Behalf Of Marcel Swart marcel.swa= rt^^^icrea.cat
Sent: Saturday, September 28, 2013 1:55 PM
T= o: Van Dam, Hubertus J
Subject: CCL: Compiling nwchem-6.3 in = redhat linux

&nb= sp;

You could try with:

 

export LARGE_FILES=3Dtrue

e= xport NWCHEM_TOP=3D/home/user1/nwchem

export NWCHEM_TARGET=3DLINUX64

export NWCHEM_MODULES=3D"smallqm"

 

export FC=3Dmpif90

expo= rt CC=3Dmpicc

 

export USE_MPI=3D"y"

 

export MPI_LOC=3D$OMPI

export MPI_LIB=3D$MPI_LOC/lib64

export MPI_INCLUDE=3D$MPI_LOC/include

<= div>

 

export BLASOPT=3D" "

 

cd $NWCHEM_TOP

./contrib/distro-tools/build_nw= chem

 

On 28 Sep 2013, at 18:41, John Keller jwk= eller^alaska.edu <owner-chemistry-.-ccl.net> wrote:



=

Dear Shilpi,

This request should go to the NWChem communi= ty/compiling users forum. The NWChem developers answer compile questions di= rectly on that forum.

http://www.nwchem-sw.org/index.php/Special:AWCforum

John Keller

University of Alaska Fairb= anks

 

On Sat, Sep 28, 2013 = at 3:23 AM, Shilpi V shilpigre-*-gmail.com <owner-= chemistry#,#ccl.net> wrote:


Sent to CCL by: "Shilpi  V" [shilpigre---gmail.com]
Dear all,=
I have tried installing Nwchem-6.3 following the instructions given in = the INSTALL file.
I did the following steps

make -v
export LAR= GE_FILES TRUE
export USE_NOFSCHECK TRUE
export TCGRSH=3D/usr/local/bi= n/ssh
export NWCHEM_TOP=3D/home/user1/nwchem
export NWCHEM_TARGET LIN= UX64
cd $NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES=3Dpnnl
m= ake >& make.log

Here, the make.log gives the following,
config/makefile.h:145: /home/user1/nwchem/-6.3/src/config/nwchem_config.h= : No such file or directory

-----
You must set NWCHEM_MODULES to = the list of modules to be included in NWChem builds.

The following m= odules are known:
NWints atomscf ddscf develop gradients moints nwdft nw= xc rimp2 stepper driver optim scfaux cphf ccsd vib mcscf prepar esp hessian= plane_wave selci dplot mp2_grad oimp2 qhop property nwpw fft rimp2_grad py= thon argos analyz diana nwmd cafe space drdy vscf uccsdt qmmm rism qmd etra= ns tce geninterface bq cons perfm dntmc transport smd nbo dangchang leps cc= ca

The following shorthand names are also recognized:
all qm md c= lassical tps alldev pnnl pnnldev smallqm
You must define NWCHEM_TARGET i= n your environment to be the name
of the machine you wish to build for .= .. for example
setenv NWCHEM_TARGET SOLARIS
Known targets are SOLARIS= , SGI_N32, ...
See the INSTALL instructions for a complete list
make:= *** [error2] Error 2

Please, make me get rid of this error and inst= all Nwchem successfully.

Thank You,

V. Shilpi



= -=3D This is automatically added to each message by the mailing script =3D-=




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Prof. Dr. Marcel Swart

ICREA Research Professor at
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= --_000_FDD09CBD8676AE40957DCDAD24E9627A0191E9EE5E19EMAIL04pnlg_-- From owner-chemistry@ccl.net Tue Oct 1 15:20:01 2013 From: "Guenter Grethe ggrethe\a/att.net" To: CCL Subject: CCL: CINF - InfoChem/Springer Scholarships Message-Id: <-49214-131001143439-6326-bvUGZXQ54wNX6W7bCBH09w:+:server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 1 Oct 2013 14:34:38 -0400 Sent to CCL by: "Guenter Grethe" [ggrethe~~att.net] Last Call - Deadline is October 7, 2013 CINF Scholarship for Scientific Excellence Co-sponsored by InfoChem and Springer The international scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) co-sponsored by InfoChem (www.infochem.de) and Springer (www.springer.com) is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 247th ACS National Meeting in Dallas, TX, March 16 20, 2014. Applicants must be enrolled at a certified college or university and must present a poster during the Welcoming Reception of the division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe-,-att.net, that you are applying for a scholarship. Submit your abstract at http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program in the session CINF Scholarship for Scientific Excellence. PACS will be open for abstract submissions on August 12, 2013, and close on October 7, 2013. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by January 31, 2014. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the Sunday reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Guenter Grethe