From w2agz at pacbell.net Wed Feb 6 05:23:32 2008 From: w2agz at pacbell.net (Paul M. Grant) Date: Tue, 5 Feb 2008 20:23:32 -0800 Subject: [xcrysden] Installing XCrySDen under YDL on IBM Core PS3 Message-ID: <00a001c86878$09147900$1b3d6b00$@net> Tone, after downloading "latest," I now get the following errors: #------------------------------# # # # Compiling XCRYSDEN C-code # # # #------------------------------# cd C; make "TOPDIR=/home/pmpgrant/XCrySDen-pre1.5bs-all" compile make[1]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/C' make TOPDIR=/home/pmpgrant/XCrySDen-pre1.5bs-all make[2]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/C' gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c detnsplit.c gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcAppInit.c In file included from xcAppInit.c:23: togl.h:48:19: error: tcl.h: No such file or directory togl.h:49:18: error: tk.h: No such file or directory In file included from xcAppInit.c:23: togl.h:106: error: expected ?)? before ?*? token togl.h:133: error: expected ?)? before ?*? token togl.h:147: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?*? token togl.h:148: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?Togl_TkWin? togl.h:189: error: expected ?)? before ?clientData? togl.h:190: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?Togl Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20080205/b80a21de/attachment.htm From tone.kokalj at ijs.si Wed Feb 6 09:34:58 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 06 Feb 2008 09:34:58 +0100 Subject: [xcrysden] Installing XCrySDen under YDL on IBM Core PS3 In-Reply-To: <00a001c86878$09147900$1b3d6b00$@net> References: <00a001c86878$09147900$1b3d6b00$@net> Message-ID: <1202286898.6334.11.camel@assam.ijs.si> On Tue, 2008-02-05 at 20:23 -0800, Paul M. Grant wrote: > Tone, after downloading ?latest,? I now get the following errors: > > #------------------------------# > > # # > > # Compiling XCRYSDEN C-code # > > # # > > #------------------------------# > > cd C; make "TOPDIR=/home/pmpgrant/XCrySDen-pre1.5bs-all" compile > > make[1]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/C' > > make TOPDIR=/home/pmpgrant/XCrySDen-pre1.5bs-all > > make[2]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/C' > > gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c detnsplit.c > > gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcAppInit.c > > In file included from xcAppInit.c:23: > > togl.h:48:19: error: tcl.h: No such file or directory > > togl.h:49:18: error: tk.h: No such file or directory Which means that tcl.h and tk.h were not found. First find where they are and then adapt Make.sys accordingly. For example, on my computer they are in /usr/include/tcl8.4/, hence I would set in Make.sys: TCL_INCDIR = -I/usr/include/tcl8.4 Regards, Tone From aryjunior at gmail.com Tue Feb 12 21:24:48 2008 From: aryjunior at gmail.com (Ary Junior) Date: Tue, 12 Feb 2008 18:24:48 -0200 Subject: [xcrysden] pw.inp question Message-ID: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> Hi, when I try: xcrysden --pwi input.pw.inp I get an error. I've checked my "xcrys_tmp/" directory and the " pwi2xsf.xsf_out" for the structure was generated, but the " pwi2xsf.xsf_out.raw" was not... Anybody can help me? The error is: Running on platform: unix Executing: /opt/XCrySDen-1.4.1bin-static/bin/ftnunit *** the hardware does not support the stereo *** TEXT-WIDGET: .a1.f1.t Executing: sh /opt/XCrySDen-1.4.1bin-static/scripts/pwi2xsf.sh /home/aryjr/DFT-GFQSI-ARY/Praticas/semicondutores/si-modelo.pw.inp Error in startup script: error opening files: ~/xcrys_tmp/xc_4618/pwi2xsf.xsf_out and ~/xcrys_tmp/xc_4618/pwi2xsf.xsf_out.raw while executing "exec $system(BINDIR)/xsf2xsf $filedir $filedir.raw 3" ("eval" body line 1) invoked from within "eval {exec $system(BINDIR)/xsf2xsf $filedir $filedir.raw} $xcMisc(reduce_to)" (procedure "xsfOpen" line 26) invoked from within "xsfOpen $program_output .mesa" (procedure "openExtStruct" line 183) invoked from within "openExtStruct 3 crystal external [list sh $system(TOPDIR)/scripts/pwi2xsf.sh] pwi2xsf.xsf_out {PWSCF Input File} ANGS -file $filedir -preset pwIn..." invoked from within "if [file exists $filedir] { # pop-up Viewer ViewMol . openExtStruct 3 crystal external [list sh $system(TOPDIR)/scripts/pwi2xsf.sh] pwi2xsf..." ("--pwi" arm line 2) invoked from within "switch -glob -- $tag { "-a" - "--attrib*" { set load_attributes 1 set file_attributes $filedir } "--xsf" - "--xcr..." (procedure "parseComLinArg" line 44) invoked from within "parseComLinArg [lrange $argv 2 end]" invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/opt/XCrySDen-1.4.1bin-static/Tcl/xcInit.tcl" line 532) Thanks very much!!! Ary Junior -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20080212/c4be5bcb/attachment.htm From w2agz at pacbell.net Wed Feb 13 07:20:53 2008 From: w2agz at pacbell.net (Paul M. Grant) Date: Tue, 12 Feb 2008 22:20:53 -0800 Subject: [xcrysden] Installing XCrySDen under YDL on IBM Core PS3 In-Reply-To: <1202286898.6334.11.camel@assam.ijs.si> References: <00a001c86878$09147900$1b3d6b00$@net> <1202286898.6334.11.camel@assam.ijs.si> Message-ID: <015d01c86e08$96bf43d0$c43dcb70$@net> Tone, I'm still having problems. Below is terminal output at the end of a long compile of "latest" on my PS3 with Possibility - 1 selected in (plain vanilla) Make.sys (compile everything...Tcl/Tk/Mesa). If I had to guess, it's as if I'm missing a "Make.sys" or "config" that's compatible with the ppc core processor in the PS3...I do see there is a BlueGene config available, but I don't know how to invoke it. *************************** . . . sunos5-smp sunos5-v8 sunos5-v8-static sunos5-v9 sunos5-v9-cc-g++ sunos5-v9-static ultrix-gcc Then type 'make ' (ex: 'make linux-x86') (ignore the following error message) make[2]: *** [configs/current] Error 1 make[2]: Leaving directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/external/src/Mesa-7.0.2' make[2]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/external/src/Mesa-7.0.2' make[3]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/external/src/Mesa-7.0.2/src' Makefile:5: ../configs/current: No such file or directory make[3]: *** No rule to make target `../configs/current'. Stop. make[3]: Leaving directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/external/src/Mesa-7.0.2/src' make[2]: *** [install] Error 1 make[2]: Leaving directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/external/src/Mesa-7.0.2' make[1]: *** [mesa] Error 2 make[1]: Leaving directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/external/src' make: *** [mesa] Error 2 [pmpgrant at W2AGZ-PS3 XCrySDen-pre1.5bs-all]$ Paul M. Grant, PhD Principal, W2AGZ Technologies Visiting Scholar, Applied Physics, Stanford University EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus w2agz at pacbell.net http://www.w2agz.com ? ? -----Original Message----- From: xcrysden-bounces at democritos.it [mailto:xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj Sent: Wednesday, February 06, 2008 12:35 AM To: XCrySDen mailing list Subject: Re: [xcrysden] Installing XCrySDen under YDL on IBM Core PS3 On Tue, 2008-02-05 at 20:23 -0800, Paul M. Grant wrote: > Tone, after downloading ?latest,? I now get the following errors: > > #------------------------------# > > # # > > # Compiling XCRYSDEN C-code # > > # # > > #------------------------------# > > cd C; make "TOPDIR=/home/pmpgrant/XCrySDen-pre1.5bs-all" compile > > make[1]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/C' > > make TOPDIR=/home/pmpgrant/XCrySDen-pre1.5bs-all > > make[2]: Entering directory `/home/pmpgrant/XCrySDen-pre1.5bs-all/C' > > gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c detnsplit.c > > gcc -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c xcAppInit.c > > In file included from xcAppInit.c:23: > > togl.h:48:19: error: tcl.h: No such file or directory > > togl.h:49:18: error: tk.h: No such file or directory Which means that tcl.h and tk.h were not found. First find where they are and then adapt Make.sys accordingly. For example, on my computer they are in /usr/include/tcl8.4/, hence I would set in Make.sys: TCL_INCDIR = -I/usr/include/tcl8.4 Regards, Tone _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From tone.kokalj at ijs.si Wed Feb 13 08:43:14 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 Feb 2008 08:43:14 +0100 Subject: [xcrysden] pw.inp question In-Reply-To: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> References: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> Message-ID: <1202888594.3367.1.camel@assam.ijs.si> On Tue, 2008-02-12 at 18:24 -0200, Ary Junior wrote: > Hi, when I try: > > xcrysden --pwi input.pw.inp > > I get an error. I've checked my "xcrys_tmp/" directory and the > "pwi2xsf.xsf_out" for the structure was generated, but the > "pwi2xsf.xsf_out.raw" was not... Anybody can help me? Please send me your PWscf input file. I'll check what is going on. (without the file, it is not possible to provide any help) Regards, Tone From tone.kokalj at ijs.si Wed Feb 13 10:42:32 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 Feb 2008 10:42:32 +0100 Subject: [xcrysden] Installing XCrySDen under YDL on IBM Core PS3 In-Reply-To: <015d01c86e08$96bf43d0$c43dcb70$@net> References: <00a001c86878$09147900$1b3d6b00$@net> <1202286898.6334.11.camel@assam.ijs.si> <015d01c86e08$96bf43d0$c43dcb70$@net> Message-ID: <1202895752.3367.18.camel@assam.ijs.si> On Tue, 2008-02-12 at 22:20 -0800, Paul M. Grant wrote: > Tone, I'm still having problems. Below is terminal output at the end of a > long compile of "latest" on my PS3 with Possibility - 1 selected in (plain > vanilla) Make.sys (compile everything...Tcl/Tk/Mesa). The compilation of all included libraries + xcrysden rarely works "out of the box". I would suggest to compile libraries separately (if needed at all). Since you have linux, you can install all the needed libraries from the linux distribution packages. You will need development packages for tcl/tk, and Mesa(OpenGL). For yellow-dog you need this packages: tcl-devel , tk-devel , mesa-libGL-devel , mesa-libGLU-devel . Once you install this packages, you need to adopt xcrysden's Make.sys accordingly, and then execute: make xcrysden (which will compile only xcrysden's code). Regards, Tone From aryjunior at gmail.com Wed Feb 13 12:05:28 2008 From: aryjunior at gmail.com (Ary Junior) Date: Wed, 13 Feb 2008 09:05:28 -0200 Subject: [xcrysden] pw.inp question In-Reply-To: <1202888594.3367.1.camel@assam.ijs.si> References: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> <1202888594.3367.1.camel@assam.ijs.si> Message-ID: <4c9c61c20802130305l2f927e0dq2cc3b12fec9574b8@mail.gmail.com> Ok, but the problem happens in a few machines in the lab, not all... The pw.inp file is OK... I'm using Debian 4.0 and after an upgrade, the software has stopped working... I'm trying to understand what package is responsible for it... Thanks very much!!! On 2/13/08, Tone Kokalj wrote: > > On Tue, 2008-02-12 at 18:24 -0200, Ary Junior wrote: > > Hi, when I try: > > > > xcrysden --pwi input.pw.inp > > > > I get an error. I've checked my "xcrys_tmp/" directory and the > > "pwi2xsf.xsf_out" for the structure was generated, but the > > "pwi2xsf.xsf_out.raw" was not... Anybody can help me? > > > Please send me your PWscf input file. I'll check what is going on. > (without the file, it is not possible to provide any help) > > Regards, Tone > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20080213/676a8d7b/attachment.htm From tone.kokalj at ijs.si Wed Feb 13 12:42:05 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 Feb 2008 12:42:05 +0100 Subject: [xcrysden] pw.inp question In-Reply-To: <4c9c61c20802130305l2f927e0dq2cc3b12fec9574b8@mail.gmail.com> References: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> <1202888594.3367.1.camel@assam.ijs.si> <4c9c61c20802130305l2f927e0dq2cc3b12fec9574b8@mail.gmail.com> Message-ID: <1202902929.3367.24.camel@assam.ijs.si> On Wed, 2008-02-13 at 09:05 -0200, Ary Junior wrote: > Ok, but the problem happens in a few machines in the lab, not all... > The pw.inp file is OK... I'm using Debian 4.0 and > after an upgrade, the software has stopped working... I'm trying to > understand what package is responsible for it... Your are right, if this has happened after system upgrade, it has to be some software-related issue. Actually, the version 1.4.1 is a bit outdated, hence you may try the "latest" version, i.e.: http://www.xcrysden.org/download/xc-latest-linuxPC-semishared.tar.gz Regards, Tone PS: I am using Debian as well (hence I would be surprised if the problem will persist) From aryjunior at gmail.com Wed Feb 13 13:25:52 2008 From: aryjunior at gmail.com (Ary Junior) Date: Wed, 13 Feb 2008 10:25:52 -0200 Subject: [xcrysden] pw.inp question In-Reply-To: <1202902929.3367.24.camel@assam.ijs.si> References: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> <1202888594.3367.1.camel@assam.ijs.si> <4c9c61c20802130305l2f927e0dq2cc3b12fec9574b8@mail.gmail.com> <1202902929.3367.24.camel@assam.ijs.si> Message-ID: <4c9c61c20802130425h65606e0fs2282f36a6acf185@mail.gmail.com> Thanks for your answer Tone, but the problem persist... If I try to execute by hands: /opt/XCrySDen-pre1.5bbin-semishared/bin/xsf2xsf ~/xcrys_tmp/xc_10580/pwi2xsf.xsf_out ~/xcrys_tmp/xc_10580/pwi2xsf.xsf_out.raw 3 The file pwi2xsf.xsf_out.raw was generated with content: DIM-GROUP 3 1 PRIMVEC 0.000000000 2.714999457 2.714999457 2.714999457 0.000000000 2.714999457 2.714999457 2.714999457 0.000000000 CONVVEC 0.000000000 2.714999457 2.714999457 2.714999457 0.000000000 2.714999457 2.714999457 2.714999457 0.000000000 PRIMCOORD 2 1 14 0.000000000 0.000000000 0.000000000 14 1.357499729 1.357499729 1.357499729 []s Ary Junior On Feb 13, 2008 9:42 AM, Tone Kokalj wrote: > On Wed, 2008-02-13 at 09:05 -0200, Ary Junior wrote: > > Ok, but the problem happens in a few machines in the lab, not all... > > The pw.inp file is OK... I'm using Debian 4.0 and > > after an upgrade, the software has stopped working... I'm trying to > > understand what package is responsible for it... > > Your are right, if this has happened after system upgrade, it has to be > some software-related issue. Actually, the version 1.4.1 is a bit > outdated, hence you may try the "latest" version, i.e.: > > http://www.xcrysden.org/download/xc-latest-linuxPC-semishared.tar.gz > > Regards, Tone > > PS: I am using Debian as well (hence I would be surprised if the problem > will persist) > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20080213/249be55e/attachment.htm From aryjunior at gmail.com Wed Feb 13 13:44:17 2008 From: aryjunior at gmail.com (Ary Junior) Date: Wed, 13 Feb 2008 10:44:17 -0200 Subject: [xcrysden] pw.inp question In-Reply-To: <4c9c61c20802130425h65606e0fs2282f36a6acf185@mail.gmail.com> References: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> <1202888594.3367.1.camel@assam.ijs.si> <4c9c61c20802130305l2f927e0dq2cc3b12fec9574b8@mail.gmail.com> <1202902929.3367.24.camel@assam.ijs.si> <4c9c61c20802130425h65606e0fs2282f36a6acf185@mail.gmail.com> Message-ID: <4c9c61c20802130444n10ad2f04tb09c76f60c444efd@mail.gmail.com> Hi Tone, the problem is solved... when I set in ~/.bashrc: XCRYSDEN_TOPDIR=/usr/local/XCrySDen-1.4.1bin-static XCRYSDEN_SCRATCH=/home/aryjr/xcrys_tmp export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" Thanks very much!!! On Feb 13, 2008 10:25 AM, Ary Junior wrote: > Thanks for your answer Tone, but the problem persist... If I try to > execute by hands: > > /opt/XCrySDen-pre1.5bbin-semishared/bin/xsf2xsf > ~/xcrys_tmp/xc_10580/pwi2xsf.xsf_out > ~/xcrys_tmp/xc_10580/pwi2xsf.xsf_out.raw 3 > > The file pwi2xsf.xsf_out.raw was generated with content: > > DIM-GROUP > 3 1 > > PRIMVEC > 0.000000000 2.714999457 2.714999457 > 2.714999457 0.000000000 2.714999457 > 2.714999457 2.714999457 0.000000000 > > CONVVEC > 0.000000000 2.714999457 2.714999457 > 2.714999457 0.000000000 2.714999457 > 2.714999457 2.714999457 0.000000000 > > PRIMCOORD > 2 1 > 14 0.000000000 0.000000000 0.000000000 > 14 1.357499729 1.357499729 1.357499729 > > []s > > Ary Junior > > > On Feb 13, 2008 9:42 AM, Tone Kokalj wrote: > > > On Wed, 2008-02-13 at 09:05 -0200, Ary Junior wrote: > > > Ok, but the problem happens in a few machines in the lab, not all... > > > The pw.inp file is OK... I'm using Debian 4.0 and > > > after an upgrade, the software has stopped working... I'm trying to > > > understand what package is responsible for it... > > > > Your are right, if this has happened after system upgrade, it has to be > > some software-related issue. Actually, the version 1.4.1 is a bit > > outdated, hence you may try the "latest" version, i.e.: > > > > http://www.xcrysden.org/download/xc-latest-linuxPC-semishared.tar.gz > > > > Regards, Tone > > > > PS: I am using Debian as well (hence I would be surprised if the problem > > will persist) > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20080213/bca7bd0f/attachment.htm From tone.kokalj at ijs.si Wed Feb 13 15:29:26 2008 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 Feb 2008 15:29:26 +0100 Subject: [xcrysden] pw.inp question In-Reply-To: <4c9c61c20802130444n10ad2f04tb09c76f60c444efd@mail.gmail.com> References: <4c9c61c20802121224k7afb1a24gcff98c45e30eb3cb@mail.gmail.com> <1202888594.3367.1.camel@assam.ijs.si> <4c9c61c20802130305l2f927e0dq2cc3b12fec9574b8@mail.gmail.com> <1202902929.3367.24.camel@assam.ijs.si> <4c9c61c20802130425h65606e0fs2282f36a6acf185@mail.gmail.com> <4c9c61c20802130444n10ad2f04tb09c76f60c444efd@mail.gmail.com> Message-ID: <1202912967.3367.39.camel@assam.ijs.si> On Wed, 2008-02-13 at 10:44 -0200, Ary Junior wrote: > Hi Tone, the problem is solved... when I set in ~/.bashrc: > > XCRYSDEN_TOPDIR=/usr/local/XCrySDen-1.4.1bin-static > XCRYSDEN_SCRATCH=/home/aryjr/xcrys_tmp > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts: > $XCRYSDEN_TOPDIR/util" > > Thanks very much!!! I don't understand. You did what? Regards, Tone