Problem compilation

[ebioman]

Hi
I got some compiling problems with this version which I did not experience earlier. I am on a CentOS based system and with Hdf >= 1.8 , g++ (GCC) 4.9.1.
There quite a few warnings regarding some pointers in hdf libraries but which causes then exit errors is:

g++ -g -O3  -Wno-div-by-zero -I ../common -I /software/include/  -fpermissive -static  -I ../common -I /software/include/  bin/GuidedAlign.o  -o bin/guidedalign -L/software/lib64/ -lhdf5_cpp -lhdf5 -lz -lpthread
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb08): undefined reference to `dlopen'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb1a): undefined reference to `dlerror'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb3a): undefined reference to `dlsym'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__search_table':
(.text+0xeef): undefined reference to `dlsym'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__close':
(.text+0x1004): undefined reference to `dlclose'
collect2: error: ld returned 1 exit status

Any idea how I can fix that ?

[mchaisso]

I pushed a fix that explicitly loads dl for hdf linked code, and actually just removed the program that was causing this particular error. I don't have access to a CentOS box to test on, but let me know if this works.

-mark

[ebioman]

Thanks for this quick reply!
It does indeed fix many of these errors but for 2 they are still left:

Still, it compiled blasr and I gave it a try but obviously it did not compile correctly and I got errors:

*** Error in `../../../blasr-master/alignment/bin/blasr': double free or corruption (!prev):     0x0000000003b52fb0 ***
======= Backtrace: =========
[0x85a513]
[0x861aa8]
[0x866687]
[0x495d5b]
[0x497d50]
[0x40ceb6]
[0x83eb13]
[0x4118ac]
======= Memory map: ========
00400000-00bcf000 r-xp 00000000 00:1d 2905236918                             /scratch/ul/monthly/eschmid/blasr-master/alignment/bin/blasr
00dcf000-00ddc000 rw-p 007cf000 00:1d 2905236918                             /scratch/ul/monthly/eschmid/blasr-master/alignment/bin/blasr
00ddc000-00df9000 rw-p 00000000 00:00 0 
0109c000-03fbe000 rw-p 00000000 00:00 0                                  [heap]
7fddc8000000-7fddc8021000 rw-p 00000000 00:00 0 
7fddc8021000-7fddcc000000 ---p 00000000 00:00 0 
7fddcc000000-7fddcc021000 rw-p 00000000 00:00 0 

and so on....

Here are some of the compilation warnings and errors:

In file included from ../common/data/hdf/HDFGroup.h:8:0,
             from ../common/data/hdf/DatasetCollection.h:8,
             from ../common/data/hdf/HDFBasReader.h:8,
             from FilterBySubreadAgreement.cpp:1:
../common/data/hdf/HDFAttributable.h: In member function ‘void     HDFAttributable::StoreAttributeNames(H5::H5Object&, std::vector<std::basic_string<char> >&)’:
../common/data/hdf/HDFAttributable.h:26:46: warning: invalid conversion from ‘void (*)    (H5::H5Object&, std::string, void*) {aka void (*)(H5::H5Object&, std::basic_string<char>, void*)}’ to     ‘H5::attr_operator_t {aka void (*)(H5::H5Location&, std::basic_string<char>, void*)}’ [-fpermissive]
               bounds, (void*) &attributeNames);
                                          ^
In file included from /software/include/H5Cpp.h:25:0,
             from ../common/data/hdf/HDFGroup.h:7,
             from ../common/data/hdf/DatasetCollection.h:8,
             from ../common/data/hdf/HDFBasReader.h:8,
             from FilterBySubreadAgreement.cpp:1:
/software/include/H5Location.h:85:6: note: initializing argument 1 of ‘int     H5::H5Location::iterateAttrs(H5::attr_operator_t, unsigned int*, void*)’
  int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
  ^
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb08): undefined reference to `dlopen'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb1a): undefined reference to `dlerror'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb3a): undefined reference to `dlsym'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__search_table':
(.text+0xeef): undefined reference to `dlsym'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__close':
(.text+0x1004): undefined reference to `dlclose'
collect2: error: ld returned 1 exit status
make[1]: *** [bin/filterBySubreadAgreement] Error 1
Makefile:148: warning: overriding commands for target `clean'
../make.rules:25: warning: ignoring old commands for target `clean'
In file included from ../common/data/hdf/HDFGroup.h:8:0,
             from ../common/data/hdf/HDFAtom.h:12,
             from ../common/data/hdf/HDFCmpFile.h:15,
             from LoadPulses.cpp:3:
../common/data/hdf/HDFAttributable.h: In member function ‘void     HDFAttributable::StoreAttributeNames(H5::H5Object&, std::vector<std::basic_string<char> >&)’:
../common/data/hdf/HDFAttributable.h:26:46: warning: invalid conversion from ‘void (*)    (H5::H5Object&, std::string, void*) {aka void (*)(H5::H5Object&, std::basic_string<char>, void*)}’ to     ‘H5::attr_operator_t {aka void (*)(H5::H5Location&, std::basic_string<char>, void*)}’ [-fpermissive]
               bounds, (void*) &attributeNames);


In file included from /software/include/H5Cpp.h:25:0,
             from ../common/data/hdf/HDFGroup.h:7,
             from ../common/data/hdf/DatasetCollection.h:8,
             from ../common/data/hdf/HDFBasReader.h:8,
             from ../common/files/ReaderAgglomerate.h:13,
             from StoreQualityByContext.cpp:1:
/software/include/H5Location.h:85:6: note: initializing argument 1 of ‘int     H5::H5Location::iterateAttrs(H5::attr_operator_t, unsigned int*, void*)’
  int iterateAttrs(attr_operator_t user_op, unsigned* idx = NULL, void* op_data = NULL);
      ^
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb08): undefined reference to `dlopen'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb1a): undefined reference to `dlerror'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__open':
(.text+0xb3a): undefined reference to `dlsym'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__search_table':
(.text+0xeef): undefined reference to `dlsym'
/software/lib64//libhdf5.a(H5PL.o): In function `H5PL__close':
(.text+0x1004): undefined reference to `dlclose'
collect2: error: ld returned 1 exit status
make[1]: *** [bin/storeQualityByContext] Error 1
Makefile:80: warning: overriding commands for target `clean'

[mchaisso]

Ok, the compilation should be fixed for the whole tree. The memory problem above is a bigger issue that I do not see on my test data. Do you have a small input fastq and the reference to share? We can take this offline at mchaisso@uw.edu to set up data transfer.

[ebioman]

Hi
Sorry for the late reply, I was busy. Indeed the previous errors are fixed now - thanks!
Now only warnings are left and it compiles otherwise.
I still receive though sudden crashes and segmentation faults. I believe that the problem stems from
the compilation with the new g++ (GCC) 4.9.1. It is much more greedy concerning variables which are not well defined. This was e.g. as well the case for the tools from Gene Meyers (DAZZLER) prior he cleaned it. Essentially if a variable is not correctly defined it will pick up a random one from the memory which leads randomly to segmentation faults. Old compilers are more forgiving since they assign 0 by default.
Therefore I receive many warnings that variables are not correctly defined and there are many voids.
Please correct me if this is all bullshit ;)
Cheers

[mchaisso]

Thanks for the update. I'll see if I can upgrade gcc here and test this out to fix this.