Re: [scipion-users] [EXT] Re: Problem compiling xmipp in Scipion3 on Centos 7 cluster

[Thu N. <t.n...@un...>]

Thank you for taking the time to help.

Despite so many trials, the problem is still showings.

Here are some more details in response to your query:

cd /usr/lib64; ls -la libhdf*
lrwxrwxrwx 1 root root      20 Mar 17 09:56 libhdf5_cpp.so -> libhdf5_cpp.so.8.0.1
lrwxrwxrwx 1 root root      20 Mar 17 09:56 libhdf5_cpp.so.8 -> libhdf5_cpp.so.8.0.1
-rwxr-xr-x 1 root root  347960 Sep 16 12:28 libhdf5_cpp.so.8.0.1
lrwxrwxrwx 1 root root      24 Mar 17 09:56 libhdf5_fortran.so -> libhdf5_fortran.so.8.0.1
lrwxrwxrwx 1 root root      24 Mar 17 09:56 libhdf5_fortran.so.8 -> libhdf5_fortran.so.8.0.1
-rwxr-xr-x 1 root root  266216 Sep 16 12:28 libhdf5_fortran.so.8.0.1
lrwxrwxrwx 1 root root      23 Mar 17 09:56 libhdf5_hl_cpp.so -> libhdf5_hl_cpp.so.8.0.1
lrwxrwxrwx 1 root root      23 Mar 17 09:56 libhdf5_hl_cpp.so.8 -> libhdf5_hl_cpp.so.8.0.1
-rwxr-xr-x 1 root root   11352 Sep 16 12:28 libhdf5_hl_cpp.so.8.0.1
lrwxrwxrwx 1 root root      26 Mar 17 09:56 libhdf5hl_fortran.so -> libhdf5hl_fortran.so.8.0.1
lrwxrwxrwx 1 root root      26 Mar 17 09:56 libhdf5hl_fortran.so.8 -> libhdf5hl_fortran.so.8.0.1
-rwxr-xr-x 1 root root   82808 Sep 16 12:28 libhdf5hl_fortran.so.8.0.1
lrwxrwxrwx 1 root root      19 Mar 17 09:56 libhdf5_hl.so -> libhdf5_hl.so.8.0.1
lrwxrwxrwx 1 root root      19 Mar 17 09:56 libhdf5_hl.so.8 -> libhdf5_hl.so.8.0.1
-rwxr-xr-x 1 root root  132536 Sep 16 12:28 libhdf5_hl.so.8.0.1
-rw-r--r-- 1 root root    4283 Sep 16 12:28 libhdf5.settings
lrwxrwxrwx 1 root root      16 Mar 17 09:56 libhdf5.so -> libhdf5.so.8.0.1
lrwxrwxrwx 1 root root      16 Mar 17 09:56 libhdf5.so.8 -> libhdf5.so.8.0.1
-rwxr-xr-x 1 root root 2796496 Sep 16 12:28 libhdf5.so.8.0.1

cd /usr/include; ls -la hdf*
-rw-r--r-- 1 root root 2655 Sep 16 12:28 hdf5.h
-rw-r--r-- 1 root root 1604 Sep 16 12:28 hdf5_hl.h

cd /share/apps/anaconda3/envs/scipion3/lib; ls -la libhdf*
ls: cannot access libhdf*: No such file or directory

cd /share/apps/anaconda3/envs/scipion3/include; ls
curses.h     form.h                 ks_names.h     ncurses.h    sqlite3ext.h       tclOO.h            tclUnixPort.h  tk3d.h      tkEntry.h         tkIntXlibDecls.h     tkMacOSX.h          tkMenu.h       tkUnixDefault.h
default.h    itcl2TclOO.h           lzma           ncursesw     sqlite3.h          tclOOIntDecls.h    tdbcDecls.h    tkArray.h   tkFileFilter.h    tkMacOSXColor.h      tkMacOSXInt.h       tkPlatDecls.h  tkUnixInt.h
eti.h        itclDecls.h            lzma.h         odbcStubs.h  tclDecls.h         tclOOInt.h         tdbc.h         tkBusy.h    tkFont.h          tkMacOSXConstants.h  tkMacOSXKeysyms.h   tkPort.h       tkUnixPort.h
fakemysql.h  itcl.h                 menu.h         openssl      tcl.h              tclPlatDecls.h     tdbcInt.h      tkButton.h  tk.h              tkMacOSXCursors.h    tkMacOSXPort.h      tkScale.h      unctrl.h
fakepq.h     itclIntDecls.h         mysqlStubs.h   panel.h      tclIntDecls.h      tclPort.h          termcap.h      tkCanvas.h  tkImgPhoto.h      tkMacOSXDebug.h      tkMacOSXPrivate.h   tkScrollbar.h  zconf.h
fakesql.h    itclInt.h              nc_tparm.h     pqStubs.h    tclInt.h           tclThread.h        term_entry.h   tkColor.h   tkIntDecls.h      tkMacOSXDefault.h    tkMacOSXWm.h        tkSelect.h     zlib.h
ffi.h        itclMigrate2TclCore.h  ncurses        python3.8    tclIntPlatDecls.h  tclTomMathDecls.h  term.h         tkDecls.h   tkInt.h           tkMacOSXEvent.h      tkMacOSXXCursors.h  tkText.h
ffitarget.h  itclTclIntStubsFcn.h   ncurses_dll.h  readline     tclOODecls.h       tclTomMath.h       tic.h          tkDList.h   tkIntPlatDecls.h  tkMacOSXFont.h       tkMenubutton.h      tkUndo.h

I am also attaching the compile.log .


----------------------------------------------------------------------------------------------------------------
Thu D. Nguyen

Bio21 Institute
The University of Melbourne, Victoria 3010 Australia



Also, what do you have in:
>>
>>> ls /usr/lib64/libhdf*
>>> ls /usr/include/hdf*
>>> ls /share/apps/anaconda3/envs/scipion3/lib/libhdf*
>>
>> ls /share/apps/anaconda3/envs/scipion3/include/*
>>
>>
>>
>> Best regards,
>> Grigory
>>
>>
>> --------------------------------------------------------------------------------
>> Grigory Sharov, Ph.D.
>>
>> MRC Laboratory of Molecular Biology,
>> Francis Crick Avenue,
>> Cambridge Biomedical Campus,
>> Cambridge CB2 0QH, UK.
>> tel. +44 (0) 1223 267228
>> e-mail: gs...@mr...
>>
>>
>> On Wed, Mar 16, 2022 at 9:50 AM Grigory Sharov <sharo...@gm...>
>> wrote:
>>
>>> Hi Thu,
>>> xmipp script needs a second parameter, but anyway I suggest going step
>>> by step:
>>>
>>> 1) conda activate scipion3
>>> 2) cd /share/apps/scipion3/software/em/xmippSrc-v3.22.01.0/
>>> 3) ./xmipp cleanBin
>>> 4) edit xmipp.conf and set Verified=False
>>> 5) ./xmipp check_config -> check what it returns
>>> 6) ./xmipp compile | tee -a compile.log -> attach here compile.log
>>>
>>> Best regards,
>>> Grigory
>>>