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informatica:hp_xw4300_500_topspin13 [2015/09/28 10:57] miquel [go no funciona, exit(127)] |
informatica:hp_xw4300_500_topspin13 [2020/07/09 13:02] (current) miquel |
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| Line 963: | Line 963: | ||
| </ | </ | ||
| - | ===== expinstall ===== | + | ===== expinstall, edhead, edlock, etc. ===== |
| Executo la comanda '' | Executo la comanda '' | ||
| Line 984: | Line 984: | ||
| * :ok: '' | * :ok: '' | ||
| - | ===== Compilació dels programes AU ===== | + | ==== Tasques pendents |
| Tasques pendents per més endavant: | Tasques pendents per més endavant: | ||
| Line 1097: | Line 1097: | ||
| </ | </ | ||
| - | ===== Compilació dels programes AU ===== | + | ===== go no funciona, exit(127) |
| - | + | ||
| - | Al procés de configuració del TopSpin vaig deixar per més endavant la compilació dels programes AU | + | |
| - | * :fail: '' | + | |
| - | * :fail: '' | + | |
| - | però alguns d' | + | |
| - | + | ||
| - | ==== Registres a la Bruker Knowledge Base relacionat amb la compilació de programes AU ==== | + | |
| - | + | ||
| - | A la base de dades Bruker Knowledge Base hi ha dos registres relacionats amb la compilació de programes AU, | + | |
| - | + | ||
| - | * [[https:// | + | |
| - | * [[https:// | + | |
| - | + | ||
| - | ==== Primer intent de compilació ==== | + | |
| - | + | ||
| - | Executo la comanda '' | + | |
| - | + | ||
| - | < | + | |
| - | / | + | |
| - | collect2: ld returned 1 exit status | + | |
| - | </ | + | |
| - | + | ||
| - | Aquest error està relacionat amb [[https:// | + | |
| - | + | ||
| - | Per evitar altres problemes, també em descarrego les noves versions d' | + | |
| - | + | ||
| - | ==== Segon intent de compilació ==== | + | |
| - | + | ||
| - | L' | + | |
| - | + | ||
| - | <code diff> | + | |
| - | # diff makeau makeau.BKUP-20150923 | + | |
| - | 1c1 | + | |
| - | < #! / | + | |
| - | --- | + | |
| - | > #! / | + | |
| - | </ | + | |
| - | + | ||
| - | Per altra banda, per tenir més informació sobre el procés de compilació, | + | |
| - | + | ||
| - | < | + | |
| - | # export XWINNMRHOME=/ | + | |
| - | # export PATH=$PATH:/ | + | |
| - | # export LD_LIBRARY_PATH=/ | + | |
| - | # export LIBRARY_PATH=/ | + | |
| - | + | ||
| - | # printenv LIBRARY_PATH LD_LIBRARY_PATH XWINNMRHOME PATH | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | </ | + | |
| - | + | ||
| - | Un cop definides aquestes variables, torno a executar el programa, però encara no aconsegueix compilar el programa i dóna el següent error, | + | |
| - | + | ||
| - | < | + | |
| - | # ./makeau -show -verbose au_zg | + | |
| - | makeau | + | |
| - | OperatingSystem=LINUX | + | |
| - | Using GNU Compiler / | + | |
| - | Setup for native compiler | + | |
| - | CC=gcc | + | |
| - | LD=c++ | + | |
| - | : | + | |
| - | / | + | |
| - | / | + | |
| - | collect2: ld returned 1 exit status | + | |
| - | exit status is: 256 1 | + | |
| - | </ | + | |
| - | + | ||
| - | + | ||
| - | Provo el suggeriment que trobo [[http:// | + | |
| - | + | ||
| - | <code diff> | + | |
| - | # diff libc.so libc.so.BKUP-20150924 | + | |
| - | 5c5 | + | |
| - | < GROUP ( / | + | |
| - | --- | + | |
| - | > GROUP ( / | + | |
| - | </ | + | |
| - | + | ||
| - | Llavors, finalment aconsegueixo compilar el programa '' | + | |
| - | + | ||
| - | < | + | |
| - | # ./makeau -show -verbose au_zg | + | |
| - | makeau | + | |
| - | OperatingSystem=LINUX | + | |
| - | Using GNU Compiler / | + | |
| - | Setup for native compiler | + | |
| - | CC=gcc | + | |
| - | LD=c++ | + | |
| - | + | ||
| - | Installed RPM packages: | + | |
| - | Can't exec " | + | |
| - | + | ||
| - | used kernel release: 3.2.0-4-amd64 | + | |
| - | Known paths: | + | |
| - | Known paths: | + | |
| - | . | + | |
| - | / | + | |
| - | / | + | |
| - | /usr/sbin | + | |
| - | /usr/bin | + | |
| - | /sbin | + | |
| - | /bin | + | |
| - | / | + | |
| - | / | + | |
| - | Current environment: | + | |
| - | HOME=/ | + | |
| - | XAUTHORITY=/ | + | |
| - | SUDO_GID=1000 | + | |
| - | LD_LIBRARY_PATH=/ | + | |
| - | DISPLAY=: | + | |
| - | LIBRARY_PATH=/ | + | |
| - | _RLD_ARGS=-ignore_unresolved | + | |
| - | MAIL=/ | + | |
| - | PWD=/ | + | |
| - | LANG=en_US.utf8 | + | |
| - | USER=root | + | |
| - | XWINNMRHOME=/ | + | |
| - | LOGNAME=root | + | |
| - | USERNAME=root | + | |
| - | SHLVL=1 | + | |
| - | OLDPWD=/ | + | |
| - | _=./ | + | |
| - | PATH=.:/ | + | |
| - | COLORTERM=gnome-terminal | + | |
| - | SUDO_USER=sermnadmin | + | |
| - | LS_COLORS=rs=0: | + | |
| - | 1: | + | |
| - | 01; | + | |
| - | : | + | |
| - | ; | + | |
| - | 01; | + | |
| - | .mpeg=01; | + | |
| - | ; | + | |
| - | 1; | + | |
| - | c=00; | + | |
| - | .spx=00; | + | |
| - | SHELL=/ | + | |
| - | TERM=screen | + | |
| - | SUDO_COMMAND=/ | + | |
| - | SUDO_UID=1000 | + | |
| - | LibraryExtension: | + | |
| - | StaticLibraryExtension: | + | |
| - | SharedLibraryExtension: | + | |
| - | LibraryPath: | + | |
| - | StaticLibraryPath: | + | |
| - | SharedLibraryPath: | + | |
| - | ObjectExtension: | + | |
| - | BinaryExtension: | + | |
| - | BinaryExtension: | + | |
| - | Check for / | + | |
| - | Check for / | + | |
| - | submacro(/ | + | |
| - | No INC_FLAGS found: using default library list | + | |
| - | Used libraries: | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
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| - | | + | |
| - | | + | |
| - | | + | |
| - | Bis | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | uni | + | |
| - | par | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | Included Libraries | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
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| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| - | Combine / | + | |
| - | + | ||
| - | Include Option: -I/ | + | |
| - | + | ||
| - | + | ||
| - | chdir / | + | |
| - | Opersys=LINUX | + | |
| - | gcc -c -DLINUX_INTEL -D_REENTRANT -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE | + | |
| - | .c | + | |
| - | Using built-in specs. | + | |
| - | COLLECT_GCC=gcc | + | |
| - | Target: x86_64-linux-gnu | + | |
| - | Configured with: ../ | + | |
| - | -enable-languages=c, | + | |
| - | th-system-zlib --libexecdir=/ | + | |
| - | 7 --libdir=/ | + | |
| - | ble-gnu-unique-object --enable-plugin --enable-objc-gc --with-arch-32=i586 --with-tune=generic --enable-checking=release --build= | + | |
| - | x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu | + | |
| - | Thread model: posix | + | |
| - | gcc version 4.7.2 (Debian 4.7.2-5) | + | |
| - | COLLECT_GCC_OPTIONS=' | + | |
| - | w' ' | + | |
| - | / | + | |
| - | X_INTEL -D _REENTRANT -D _FILE_OFFSET_BITS=64 -D _LARGEFILE_SOURCE au_zg.c -quiet -dumpbase au_zg.c -m32 -mtune=generic -march=i5 | + | |
| - | 86 -auxbase au_zg -g -w -version -o / | + | |
| - | GNU C (Debian 4.7.2-5) version 4.7.2 (x86_64-linux-gnu) | + | |
| - | compiled by GNU C version 4.7.2, GMP version 5.0.5, MPFR version 3.1.0-p10, MPC version 0.9 | + | |
| - | GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 | + | |
| - | ignoring nonexistent directory "/ | + | |
| - | ignoring nonexistent directory "/ | + | |
| - | ignoring nonexistent directory "/ | + | |
| - | #include " | + | |
| - | #include <...> search starts here: | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | End of search list. | + | |
| - | GNU C (Debian 4.7.2-5) version 4.7.2 (x86_64-linux-gnu) | + | |
| - | compiled by GNU C version 4.7.2, GMP version 5.0.5, MPFR version 3.1.0-p10, MPC version 0.9 | + | |
| - | GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 | + | |
| - | Compiler executable checksum: 7fa7c2a970be5e19ce72b2057c14800d | + | |
| - | COLLECT_GCC_OPTIONS=' | + | |
| - | w' ' | + | |
| - | as -v -W -I / | + | |
| - | GNU assembler version 2.22 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.22 | + | |
| - | COMPILER_PATH=/ | + | |
| - | 86_64-linux-gnu/ | + | |
| - | LIBRARY_PATH=/ | + | |
| - | /:/ | + | |
| - | ib32/:/ | + | |
| - | 64-linux-gnu/ | + | |
| - | COLLECT_GCC_OPTIONS=' | + | |
| - | w' ' | + | |
| - | exit=0 sig=0 dump=0 | + | |
| - | Used Libraries | + | |
| - | auliba.so aulibp.so chparmod.so sxutil.so libhpcu.so libBpsu.so ConvSf.so libSwish.so libVtu.so lib_sbsb.so lib_tty.so librrs.so | + | |
| - | liblrs.so Bis.so convpw.so editpar.so libacq.so util.so aulibp.so uni.so par.so libPath.so libcb.so libUtil.so libCUtil.so libSha | + | |
| - | peIO.so libFunc.so libJCamp.so libCt.so libQTP.so auliba.a aulibp.a chparmod.a libacq.a editpar.a util.a uni.a par.a libPath.a li | + | |
| - | bcb.a | + | |
| - | c++ -m32 -Wl, | + | |
| - | / | + | |
| - | prog/ | + | |
| - | f.so / | + | |
| - | pin1.3/ | + | |
| - | /Bis.so / | + | |
| - | pin1.3/ | + | |
| - | o / | + | |
| - | / | + | |
| - | / | + | |
| - | pin1.3/ | + | |
| - | / | + | |
| - | / | + | |
| - | c++ -m32 -Wl, | + | |
| - | / | + | |
| - | prog/ | + | |
| - | f.so / | + | |
| - | pin1.3/ | + | |
| - | /Bis.so / | + | |
| - | pin1.3/ | + | |
| - | o / | + | |
| - | / | + | |
| - | / | + | |
| - | pin1.3/ | + | |
| - | / | + | |
| - | / | + | |
| - | Reading specs from / | + | |
| - | Configured with: ../ | + | |
| - | with-cpu=pentium4 | + | |
| - | Thread model: posix | + | |
| - | gcc version 3.3.5 | + | |
| - | / | + | |
| - | .so.2 -o au_zg -s / | + | |
| - | L/ | + | |
| - | -lib -L/ | + | |
| - | in1.3/ | + | |
| - | n/au_zg.o / | + | |
| - | opspin1.3/ | + | |
| - | hlib/ | + | |
| - | / | + | |
| - | prog/ | + | |
| - | / | + | |
| - | hlib/par.so / | + | |
| - | topspin1.3/ | + | |
| - | prog/ | + | |
| - | / | + | |
| - | /editpar.a / | + | |
| - | /libPath.a / | + | |
| - | lib/ | + | |
| - | exit status is: 0 0 | + | |
| - | </ | + | |
| - | + | ||
| - | i quan comprovo el fitxer creat trobo que és un executable de 32-bits | + | |
| - | + | ||
| - | < | + | |
| - | # file / | + | |
| - | / | + | |
| - | </ | + | |
| - | + | ||
| - | i si afegim a la variable // | + | |
| - | + | ||
| - | <code bash> | + | |
| - | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/ | + | |
| - | </ | + | |
| - | + | ||
| - | el programa '' | + | |
| - | + | ||
| - | < | + | |
| - | # ldd / | + | |
| - | linux-gate.so.1 => (0xf77e0000) | + | |
| - | libstdc++.so.5 => / | + | |
| - | auliba.so => / | + | |
| - | aulibp.so => / | + | |
| - | chparmod.so => / | + | |
| - | sxutil.so => / | + | |
| - | libhpcu.so => / | + | |
| - | libBpsu.so => / | + | |
| - | ConvSf.so => / | + | |
| - | libSwish.so => / | + | |
| - | libVtu.so => / | + | |
| - | lib_sbsb.so => / | + | |
| - | lib_tty.so => / | + | |
| - | librrs.so => / | + | |
| - | liblrs.so => / | + | |
| - | Bis.so => / | + | |
| - | convpw.so => / | + | |
| - | editpar.so => / | + | |
| - | libacq.so => / | + | |
| - | util.so => / | + | |
| - | uni.so => / | + | |
| - | par.so => / | + | |
| - | libPath.so => / | + | |
| - | libcb.so => / | + | |
| - | libUtil.so => / | + | |
| - | libCUtil.so => / | + | |
| - | libShapeIO.so => / | + | |
| - | libFunc.so => / | + | |
| - | libJCamp.so => / | + | |
| - | libCt.so => / | + | |
| - | libQTP.so => / | + | |
| - | libdl.so.2 => / | + | |
| - | libm.so.6 => / | + | |
| - | libgcc_s.so.1 => / | + | |
| - | libc.so.6 => / | + | |
| - | / | + | |
| - | </ | + | |
| - | + | ||
| - | De totes formes, ara hauré d' | + | |
| - | + | ||
| - | ==== Canvis addicionals al programa ' | + | |
| - | + | ||
| - | Per poder compilar els programes AU des de dins el TopSpin, caldrà comprovar si cal afegir al programa //makeau// les definicions de variables d' | + | |
| - | + | ||
| - | * LD_LIBRARY_PATH=/ | + | |
| - | * LIBRARY_PATH=/ | + | |
| - | + | ||
| - | o si n'hi ha prou amb definir-les al fitxer de configuració de l' | + | |
| - | + | ||
| - | Consultar: | + | |
| - | * [[http:// | + | |
| - | * [[https:// | + | |
| - | * [[http:// | + | |
| - | * hint: emprar la comanda '' | + | |
| - | * [[http:// | + | |
| - | * [[https:// | + | |
| - | * [[http:// | + | |
| - | + | ||
| - | ==== Canvis al TopSpin ==== | + | |
| - | + | ||
| - | === / | + | |
| - | + | ||
| - | Afegeixo la variable // | + | |
| - | + | ||
| - | <code diff> | + | |
| - | # diff topspin topspin.ORIG-20150824 | + | |
| - | 62c62 | + | |
| - | < | + | |
| - | --- | + | |
| - | > | + | |
| - | </ | + | |
| - | + | ||
| - | === / | + | |
| - | + | ||
| - | Creo el fitxer ///# more / | + | |
| - | + | ||
| - | <code bash> | + | |
| - | # MCE - 20150925 - Library path environment variables added to allow | + | |
| - | # compilating TopSpin 1.3 AU programs in newer GNU/Linux versions | + | |
| - | + | ||
| - | export PATH=$PATH:/ | + | |
| - | export LIBRARY_PATH=/ | + | |
| - | export LD_LIBRARY_PATH=/ | + | |
| - | </ | + | |
| - | + | ||
| - | ==== Compilació dels programes AU ==== | + | |
| - | + | ||
| - | Executo la comanda '' | + | |
| - | + | ||
| - | < | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | / | + | |
| - | exit 1 | + | |
| - | </ | + | |
| - | + | ||
| - | <note important> | + | |
| - | Ara que els programes AU s'han compilat correctament, | + | |
| - | + | ||
| - | < | + | |
| - | ILLEGAL TERMINATION of process 28469 | + | |
| - | due to signal 11 | + | |
| - | </ | + | |
| - | + | ||
| - | potser pels motius explicats [[http:// | + | |
| - | </ | + | |
| - | + | ||
| - | ==== go no funciona, exit(127) ==== | + | |
| L' | L' | ||
| Line 1668: | Line 1149: | ||
| Tanmateix, podria provar a descarregar-les del magatzem [[http:// | Tanmateix, podria provar a descarregar-les del magatzem [[http:// | ||
| - | ==== Manquen solvents a la comanda lock ==== | + | ===== Compilació dels programes AU ===== |
| - | Quan executo la comanda '' | + | Aquesta part és tan llarga |
| + | * [[informatica: | ||
| - | ==== Canvi de / | + | ===== Manquen solvents |
| - | Fins ara he provat a compilar/enllaçar els programes amb les biblioteques disponibles a ///lib32///, però a les futures versions de Debian multiarquitectura (per exemple, 32- i 64-bits) les biblioteques de 32-bits estaran | + | Quan executo la comanda '' |
| - | Potser convindria redefinir les variables | + | La causa de l' |
| - | La definició actual de la variable d' | + | Comprovar a la Bruker Knowledge Base els [[https://www.bruker.com/cgi-bin/bkb/ |
| + | * [[https:// | ||
| + | * [[https:// | ||
| + | * [[https:// | ||
| + | * [[https:// | ||
| - | <file> | + | <WRAP tip> |
| - | # topspin -e echo $LD_LIBRARY_PATH | + | FIXME |
| - | / | + | |
| - | </ | + | |
| - | i les biblioteques emprades pel programa AU '' | + | Explicar la solució final: |
| + | * copiar el fitxer | ||
| + | * editar els fitxers del TS13 per corregir els noms dels solvents segons el fitxer de solvents del TS31 | ||
| + | * afegir la informació dels solvents afegits després de la versió TS13 | ||
| + | </WRAP> | ||
| - | < | + | ===== Còpia dels programes AU compilats a l' |
| - | # ls -l / | + | |
| - | -rw-r--r-- 1 root root 148920 Feb 22 2015 /lib32/ | + | Mentres cerco la forma de compilar els programes AU en aquesta versió de GNU/Linux, intento una solució més immediata: copiar els fitxers AU ja compilats a l' |
| - | -rw-r--r-- 1 root root 13884 Feb 22 2015 / | + | |
| - | lrwxrwxrwx 1 root root 12 Feb 22 2015 / | + | <WRAP important> |
| - | -rw-r--r-- 1 root root 148992 Feb 22 2015 / | + | Caldrà compilar a l' |
| - | -rw-r--r-- 1 root root 13960 Feb 22 2015 /lib/ | + | </WRAP> |
| - | lrwxrwxrwx 1 root root 12 Feb 22 2015 / | + | |
| - | # ls -l / | ||
| - | -rw-r--r-- 1 root root 9768 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 13 Feb 22 2015 / | ||
| - | -rw-r--r-- 1 root root 9844 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 13 Feb 22 2015 / | ||
| - | # ls -l / | ||
| - | -rwxr-xr-x 1 root root 1445980 Feb 22 2015 / | ||
| - | -rw-r--r-- 1 root root 185852 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 15 Feb 22 2015 / | ||
| - | -rw-r--r-- 1 root root 38336 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 16 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 12 Feb 22 2015 / | ||
| - | -rwxr-xr-x 1 root root 1360008 Feb 22 2015 / | ||
| - | -rw-r--r-- 1 root root 185928 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 15 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 17 Feb 22 2015 / | ||
| - | -rw-r--r-- 1 root root 13836 Feb 22 2015 / | ||
| - | -rw-r--r-- 1 root root 38416 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 16 Feb 22 2015 / | ||
| - | lrwxrwxrwx 1 root root 12 Feb 22 2015 / | ||
| - | </ | ||