On Thu, Oct 3, 2019 at 11:20 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Oct 2, 2019 at 10:16 AM Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
> > CPPTRAJ: Multi frame strip command test.
> > File locking failed in ADIOI_Set_lock(fd A,cmd F_SETLKW/7,type
> > F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26.
> > - If the file system is NFS, you need to use NFS version 3, ensure that
> the
> > lockd daemon is running on all the machines, and mount the directory with
> > the 'noac' option (no attribute caching).
> > - If the file system is LUSTRE, ensure that the directory is mounted with
> > the 'flock' option.
> > ADIOI_Set_lock:: Function not implemented
> > ADIOI_Set_lock:offset 0, length 1
>
> This is a system error, not a cpptraj one. Are you using intel mpi? A
> brief google search indicates it may be intel mpi related. If so, try
> using a different version of intel mpi (or if you don't need parallel
> cpptraj, don't worry about it as suggested by Dave).
>
> It is intel mpi version 4.1.0. I don't need parallel cpptraj.
> /home/external/cbs/sunitap/softwares/amber18/bin/cpptraj: error while
> > loading shared libraries: libbz2.so.1.0: cannot open shared object file:
> No
> > such file or directory
>
> Another system error. Cpptraj was compiled and linked to a shared
> libbz2 library that is not present on whatever node you are running
> on. Ensure this library is present on the excuting node and/or that
> LD_LIBRARY_PATH is properly set.
>
> I am trying to install bzip2-1.0.8 from tar file with prefix option but
getting following error. I also tried compiling with -fPIC but still
getting error.
make -f Makefile-libbz2_so
gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.8 blocksort.o
huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
/usr/bin/ld: compress.o: relocation R_X86_64_32 against `.rodata.str1.8'
can not be used when making a shared object; recompile with -fPIC
compress.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [all] Error 1
> -Dan
>
> > ./runmd.sh: Program error
> > make[4]: [ntx5] Error 1 (ignored)
> > Netcdf MD restart read test, ntx=1
> > diffing md1.rst7 with md2.rst7
> > PASSED
> > ---------------------------
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Received on Fri Oct 04 2019 - 00:30:02 PDT
