could not load Parasail module needed for Smith-Waterman

[maronem]

When running perl ESPRESSO_C.pl I get the error: could not load Parasail module needed for Smith-Waterman.

I compiled Parasail using ./src/Parasail/build but got this message at the end:

[ 99%] Linking C executable test_verify_traces
[ 99%] Built target test_verify_traces
[ 99%] Building C object CMakeFiles/test_verify_cigars.dir/tests/test_verify_cigars.c.o
[100%] Linking C executable test_verify_cigars
[100%] Built target test_verify_cigars
cp: ./parasail/build/libparasail.so: No such file or directory

Is there any additional steps I need to compile or install Parasail so ESPRESSO can access the module?

[EricKutschera]

It looks like make succeeded for the parasail C library, but libparasail.so wasn't there. Did you run the build on a Mac? It could be that a .dylib was created instead of a .so

The build script was only tested for linux, but you might be able to follow the steps in the build script with .so replaced with .dylib: https://github.com/Xinglab/espresso/blob/v1.5.0/src/Parasail/build#L35

[maronem]

Appreciate the fast reply! Yes, I am running the build on an x64 Mac. I replaced .so with .dylib in the build script and it seemed to resolve that issue:

[100%] Linking C executable test_verify_cigars
[100%] Built target test_verify_cigars
Checking if your kit is complete...
Looks good
Warning: -L. changed to -L/Users/michael/espresso-1.5.0/src/Parasail/.
Generating a Unix-style Makefile
Writing Makefile for Parasail
Writing MYMETA.yml and MYMETA.json

But now I am getting an error from Parasail.bundle trying to load the libparasail.dylib library:

                        ^
100 warnings generated.
rm -f blib/arch/auto/Parasail/Parasail.bundle
LD_RUN_PATH="/Users/michael/espresso-1.5.0/src/Parasail" cc  -bundle -undefined dynamic_lookup  Parasail.o  -o blib/arch/auto/Parasail/Parasail.bundle  \
	   -L/Users/michael/espresso-1.5.0/src/Parasail -lparasail   \
	  
chmod 755 blib/arch/auto/Parasail/Parasail.bundle
"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Parasail.bs blib/arch/auto/Parasail/Parasail.bs 644
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/Parasail.t .. 1/17 
#   Failed test 'use Parasail;'
#   at t/Parasail.t line 6.
#     Tried to use 'Parasail'.
#     Error:  Can't load '/Users/michael/espresso-1.5.0/src/Parasail/blib/arch/auto/Parasail/Parasail.bundle' for module Parasail: dlopen(/Users/michael/espresso-1.5.0/src/Parasail/blib/arch/auto/Parasail/Parasail.bundle, 0x0002): Library not loaded: @rpath/libparasail.dylib
#   Referenced from: <B479F6CC-14DE-32FB-BEA8-96C534E89B34> /Users/michael/espresso-1.5.0/src/Parasail/blib/arch/auto/Parasail/Parasail.bundle
#   Reason: , (security policy does not allow @ path expansion) at /System/Library/Perl/5.30/darwin-thread-multi-2level/DynaLoader.pm line 197.
#  at t/Parasail.t line 6.
# Compilation failed in require at t/Parasail.t line 6.
# BEGIN failed--compilation aborted at t/Parasail.t line 6.
Undefined subroutine &Parasail::matrix_create called at /Users/michael/espresso-1.5.0/src/Parasail/blib/lib/Parasail.pm line 56.
# Looks like your test exited with 255 just after 1.
t/Parasail.t .. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 17/17 subtests 

Test Summary Report
-------------------
t/Parasail.t (Wstat: 65280 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 17 tests but ran 1.
Files=1, Tests=1,  1 wallclock secs ( 0.03 usr  0.02 sys +  0.11 cusr  0.07 csys =  0.23 CPU)
Result: FAIL
Failed 1/1 test programs. 1/1 subtests failed.
make: *** [test_dynamic] Error 255

I checked the Perl DynaLoader.pm script on my system and it says:

    # Many dynamic extension loading problems will appear to come from
    # this section of code: XYZ failed at line 123 of DynaLoader.pm.
    # Often these errors are actually occurring in the initialisation
    # C code of the extension XS file. Perl reports the error as being
    # in this perl code simply because this was the last perl code
    # it executed.

Not sure where to go from here.

[EricKutschera]

The main error seems to be

  Error:  Can't load '/Users/.../Parasail.bundle' for module Parasail: dlopen(/Users/.../Parasail.bundle, 0x0002): Library not loaded: @rpath/libparasail.dylib
Referenced from: <B479F6CC-14DE-32FB-BEA8-96C534E89B34> /Users/.../Parasail.bundle
Reason: , (security policy does not allow @ path expansion) at /System/.../DynaLoader.pm line 197.

As you pointed out there's a comment in DynaLoader.pm saying that the line number is not very helpful. One thing that stands out is security policy does not allow @ path expansion. I think it's trying to load @rpath/libparasail.dylib and the @rpath/ part is supposed to be a flexible way to find the .dylib, but for some reason @rpath isn't working as expected. I'm not sure about the details, but I think some compiler flags would need to be set when creating the Parasail.bundle to get @rpath to work

It seems like it may be possible to put in the full path to the .dylib to avoid the rpath issue: https://stackoverflow.com/questions/9263256/why-is-install-name-tool-and-otool-necessary-for-mach-o-libraries-in-mac-os-x

Maybe a command like install_name_tool -change @rpath/libparasail.dylib /Users/michael/espresso-1.5.0/src/Parasail/libparasail.dylib /Users/michael/espresso-1.5.0/src/Parasail/blib/arch/auto/Parasail/Parasail.bundle