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Bug #3472
closedFindEM does not work on modern OS's with newer GCC
Added by Neil Voss about 9 years ago. Updated about 9 years ago.
Start date:
08/31/2015
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:
Description
There is no clear way for me to install FindEM on Debian 8 as Fortran77 is now unsupported by GCC. The recommendation on the internet is to rewrite the code or install an older operating system.
https://bugs.launchpad.net/ubuntu/+source/gcc-3.4/+bug/249991
I downloaded the newer code from the MRC, but it did not compile. Failing on the last step.
Updated by Neil Voss about 9 years ago
Error messages:
emfacility@miracles:~$ cd newFindEM/findem emfacility@miracles:~/newFindEM/findem$ make rm -fv *~ *.mod removed ‘image_arrays.mod’ removed ‘image_arrays2.mod’ removed ‘mrc_image.mod’ #rm -fv *.o *.a rm -fv cccmaxmap001.mrc gcc -O3 -w -march=native -mtune=native -c plot2k.c ar cr ./plot2klib.a plot2k.o gfortran -O3 -w -march=native -mtune=native -c lcflib.for gfortran -O3 -w -march=native -mtune=native -c mtzlib.for miscsubs.for ar cr ./misclib.a lcflib.o mtzlib.o miscsubs.o gfortran -O3 -w -march=native -mtune=native -c imsubs2000.for gfortran -O3 -w -march=native -mtune=native -c imsubs2.for ar cr ./imlib2k.a imsubs2.o imsubs2000.o gfortran -O3 -w -march=native -mtune=native -c ifftsub.for ar cr ./ifftlib.a ifftsub.o gfortran -O3 -w -march=native -mtune=native -c unix.for diskio.for subs.for parser.for symlib.for ccplib.for gcc -c -O3 -DPROTOTYPE -Dalliant -w library.c ar cr ./genlib.a diskio.o library.o parser.o subs.o symlib.o unix.o ccplib.o gfortran -O3 -w -march=native -mtune=native -o ./findem32.exe findem.f90 ./imlib2k.a ./ifftlib.a ./genlib.a ./misclib.a ./plot2klib.a ./genlib.a(symlib.o): In function `hkleq_': symlib.for:(.text+0xd8b0): multiple definition of `hkleq_' ./genlib.a(ccplib.o):ccplib.for:(.text+0x6230): first defined here ./genlib.a(symlib.o): In function `ccp4_hash_lookup_': symlib.for:(.text+0xd8e0): multiple definition of `ccp4_hash_lookup_' ./genlib.a(ccplib.o):ccplib.for:(.text+0x6260): first defined here ./genlib.a(symlib.o): In function `ccp4_hash_setup_': symlib.for:(.text+0xd960): multiple definition of `ccp4_hash_setup_' ./genlib.a(ccplib.o):ccplib.for:(.text+0x62e0): first defined here ./genlib.a(symlib.o): In function `ccp4_hash_zeroit_': symlib.for:(.text+0xdb00): multiple definition of `ccp4_hash_zeroit_' ./genlib.a(ccplib.o):ccplib.for:(.text+0x6480): first defined here ./genlib.a(symlib.o): In function `sthlsq_': symlib.for:(.text+0xdf80): multiple definition of `sthlsq_' ./genlib.a(ccplib.o):ccplib.for:(.text+0x6520): first defined here ./genlib.a(symlib.o): In function `sts3r4_': symlib.for:(.text+0xe400): multiple definition of `sts3r4_' ./genlib.a(ccplib.o):ccplib.for:(.text+0x6550): first defined here /tmp/cc4v1T98.o: In function `correlationfft_': findem.f90:(.text+0x8bb): undefined reference to `todfft_' findem.f90:(.text+0xc11): undefined reference to `todfft_' /tmp/cc4v1T98.o: In function `convolutionfft_': findem.f90:(.text+0x1100): undefined reference to `todfft_' findem.f90:(.text+0x1451): undefined reference to `todfft_' /tmp/cc4v1T98.o: In function `getccmap_': findem.f90:(.text+0x342d): undefined reference to `todfft_' /tmp/cc4v1T98.o:findem.f90:(.text+0x3446): more undefined references to `todfft_' follow ./imlib2k.a(imsubs2000.o): In function `master.0.imopen_.part.0': imsubs2000.for:(.text+0x2678): undefined reference to `ccpupc_' ./genlib.a(diskio.o): In function `qqopen_': diskio.for:(.text+0x1dc): undefined reference to `ccpexs_' diskio.for:(.text+0x2ae): undefined reference to `ccperr_' diskio.for:(.text+0x370): undefined reference to `qprint_' diskio.for:(.text+0x448): undefined reference to `ccperr_' diskio.for:(.text+0x552): undefined reference to `ccperr_' diskio.for:(.text+0x569): undefined reference to `ccpexs_' diskio.for:(.text+0x5b8): undefined reference to `ccpupc_' diskio.for:(.text+0x682): undefined reference to `ccperr_' diskio.for:(.text+0x6a2): undefined reference to `ccperr_' ./genlib.a(diskio.o): In function `qopen_': diskio.for:(.text+0xa3e): undefined reference to `ccpupc_' diskio.for:(.text+0xb5d): undefined reference to `ccperr_' ./genlib.a(library.o): In function `ustenv_': library.c:(.text+0x507): undefined reference to `ccperr_' ./genlib.a(library.o): In function `cunlink_': library.c:(.text+0x587): undefined reference to `qprint_' ./genlib.a(library.o): In function `ccpal1_': library.c:(.text+0x770): undefined reference to `ccperr_' ./genlib.a(library.o): In function `copen_': library.c:(.text+0x1050): undefined reference to `ccperr_' library.c:(.text+0x1138): undefined reference to `ccperr_' library.c:(.text+0x122f): undefined reference to `ccperr_' library.c:(.text+0x12a8): undefined reference to `ccperr_' ./genlib.a(library.o):library.c:(.text+0x12c9): more undefined references to `ccperr_' follow ./genlib.a(unix.o): In function `ugerr_': unix.for:(.text+0x9e): undefined reference to `ierrno_' unix.for:(.text+0xe8): undefined reference to `gerror_' ./genlib.a(unix.o): In function `ccpopn_': unix.for:(.text+0x637): undefined reference to `qprint_' unix.for:(.text+0x64b): undefined reference to `qprint_' unix.for:(.text+0x769): undefined reference to `qprint_' unix.for:(.text+0x786): undefined reference to `qprint_' unix.for:(.text+0x822): undefined reference to `ccperr_' unix.for:(.text+0xada): undefined reference to `ccperr_' unix.for:(.text+0xb75): undefined reference to `ierrno_' unix.for:(.text+0x1114): undefined reference to `ccperr_' unix.for:(.text+0x1128): undefined reference to `gerror_' ./genlib.a(unix.o): In function `uisatt_': unix.for:(.text+0x13ad): undefined reference to `isatty_' ./genlib.a(unix.o): In function `ccpspw_': unix.for:(.text+0x13c3): undefined reference to `system_' ./genlib.a(ccplib.o): In function `ccpnun_': ccplib.for:(.text+0xff7): undefined reference to `ccperr_' ./genlib.a(ccplib.o): In function `ccpalc_': ccplib.for:(.text+0x107a): undefined reference to `ccpupc_' ccplib.for:(.text+0x10d5): undefined reference to `ccperr_' ccplib.for:(.text+0x10f7): undefined reference to `ccperr_' ccplib.for:(.text+0x1117): undefined reference to `ccperr_' ./genlib.a(ccplib.o): In function `ccpe2i_': ccplib.for:(.text+0x15aa): undefined reference to `ccperr_' ./genlib.a(ccplib.o): In function `ccpdpn_': ccplib.for:(.text+0x2696): undefined reference to `ccpupc_' ccplib.for:(.text+0x26a6): undefined reference to `ccpupc_' ccplib.for:(.text+0x28b1): undefined reference to `ccperr_' ccplib.for:(.text+0x2a71): undefined reference to `ccperr_' ccplib.for:(.text+0x2d28): undefined reference to `ccperr_' ./genlib.a(ccplib.o): In function `csetnv_': ccplib.for:(.text+0x4311): undefined reference to `qprint_' ccplib.for:(.text+0x4751): undefined reference to `ccperr_' ccplib.for:(.text+0x4767): undefined reference to `qprint_' ccplib.for:(.text+0x494a): undefined reference to `ccplwc_' ccplib.for:(.text+0x4fce): undefined reference to `ccperr_' ccplib.for:(.text+0x4fe9): undefined reference to `ccperr_' ccplib.for:(.text+0x5135): undefined reference to `ccperr_' ccplib.for:(.text+0x518b): undefined reference to `ccperr_' ccplib.for:(.text+0x5318): undefined reference to `ccperr_' ccplib.for:(.text+0x5a36): undefined reference to `ustime_' ccplib.for:(.text+0x5c80): undefined reference to `ccperr_' ccplib.for:(.text+0x5d24): undefined reference to `ccperr_' ./genlib.a(ccplib.o): In function `ccp4_hash_setup_': ccplib.for:(.text+0x6445): undefined reference to `ccperr_' ./genlib.a(ccplib.o): In function `lstlsq_': ccplib.for:(.text+0x6508): undefined reference to `lstlsq1_' ./genlib.a(ccplib.o): In function `sthlsq_': ccplib.for:(.text+0x6535): undefined reference to `sthlsq1_' ./genlib.a(ccplib.o): In function `sts3r4_': ccplib.for:(.text+0x6565): undefined reference to `sts3r41_' ./genlib.a(ccplib.o): In function `ccptoi_': ccplib.for:(.text+0x6011): undefined reference to `ccperr_' ./genlib.a(parser.o): In function `keynum_': parser.for:(.text+0xd1a): undefined reference to `ccperr_' parser.for:(.text+0xd61): undefined reference to `ccperr_' ./genlib.a(parser.o): In function `rdsymm_': parser.for:(.text+0x1322): undefined reference to `ccpupc_' parser.for:(.text+0x13f4): undefined reference to `ccpupc_' ./genlib.a(parser.o): In function `rdhead_': parser.for:(.text+0x1655): undefined reference to `ccpupc_' ./genlib.a(parser.o): In function `rdresl_': parser.for:(.text+0x24d0): undefined reference to `ccpupc_' ./genlib.a(parser.o): In function `rdatomselect_': parser.for:(.text+0x29e2): undefined reference to `ccpupc_' parser.for:(.text+0x2fca): undefined reference to `ccperr_' parser.for:(.text+0x3638): undefined reference to `ccpupc_' ./genlib.a(parser.o): In function `lerror_': parser.for:(.text+0x27f): undefined reference to `ccperr_' ./genlib.a(symlib.o): In function `master.0.centr_.constprop.1': symlib.for:(.text+0xa7): undefined reference to `ccperr_' ./genlib.a(symlib.o): In function `master.0.centr_.constprop.4': symlib.for:(.text+0x6da): undefined reference to `ccperr_' ./genlib.a(symlib.o): In function `fndsmp_': symlib.for:(.text+0x82f): undefined reference to `ccperr_' symlib.for:(.text+0x92f): undefined reference to `ccperr_' ./genlib.a(symlib.o):symlib.for:(.text+0xa2f): more undefined references to `ccperr_' follow ./genlib.a(symlib.o): In function `pgnlau_': symlib.for:(.text+0x184d): undefined reference to `ccpupc_' symlib.for:(.text+0x239f): undefined reference to `ccperr_' ./genlib.a(symlib.o): In function `symtr3_': symlib.for:(.text+0x2aa2): undefined reference to `ccperr_' symlib.for:(.text+0x2ac2): undefined reference to `ccperr_' symlib.for:(.text+0x2aff): undefined reference to `ccperr_' symlib.for:(.text+0x2b42): undefined reference to `ccperr_' ./genlib.a(symlib.o):symlib.for:(.text+0x2e1a): more undefined references to `ccperr_' follow ./genlib.a(symlib.o): In function `msymlb_': symlib.for:(.text+0x9040): undefined reference to `ccpupc_' symlib.for:(.text+0x9092): undefined reference to `parse_' ./genlib.a(symlib.o): In function `msymlb2_': symlib.for:(.text+0x9751): undefined reference to `ccpupc_' symlib.for:(.text+0x97a3): undefined reference to `parse_' ./genlib.a(symlib.o): In function `msymlb3_': symlib.for:(.text+0xa009): undefined reference to `ccpupc_' symlib.for:(.text+0xa064): undefined reference to `parse_' symlib.for:(.text+0xa642): undefined reference to `matmulnm_' ./genlib.a(symlib.o): In function `symtr4_': symlib.for:(.text+0xd058): undefined reference to `ccperr_' symlib.for:(.text+0xd088): undefined reference to `ccperr_' symlib.for:(.text+0xd0b8): undefined reference to `ccperr_' symlib.for:(.text+0xd0e8): undefined reference to `ccperr_' symlib.for:(.text+0xd11c): undefined reference to `ccperr_' ./genlib.a(symlib.o):symlib.for:(.text+0xd59e): more undefined references to `ccperr_' follow collect2: error: ld returned 1 exit status Makefile:19: recipe for target 'findem' failed make: *** [findem] Error 1
Updated by Anchi Cheng about 9 years ago
As I recall, mrc library relies on ccp4 library to build. Maybe that is what is missing ?
Updated by Neil Voss about 9 years ago
I found out that if I copy all the .a files from image2010, then only compile findem it works. I guess I am just not familiar with the MRC code enough.
Updated by Scott Stagg about 9 years ago
Hi Neil,
I am running into the same problem I think. I tried just "make findem", but I'm getting this error:
gcc -O3 -w -march=native -mtune=native -c plot2k.c gcc: error: plot2k.c: No such file or directory gcc: fatal error: no input files compilation terminated. make: *** [plot2k] Error 4
Did you forget to svn add plot2k.c or is something else going on?
Updated by Scott Stagg about 9 years ago
I just added the core Appion folks because this has me sort of panicked. Our HPC recently updated to RedHat 7.1, and we are trying to get the Appion nodes updated too. It seems that FindEM is not working on modern systems. Since FindEM is such a fundamental part of our workflow, we are essentially at a standstill until this gets fixed. Has anyone else run into this and figured out a work around? Is there a different template picker that other groups are using in the Appion environment?
Updated by Neil Voss about 9 years ago
First, do not type 'make findem' just type 'make' and it should work.
FindEM uses image2010 libraries from the MRC package. I decided to use their pre-compiled libraries rather than compile them ourselves.
Here is the deal, what we were doing before was not kosher, we included the source code from the MRC image2010 without permission. If we are going to compile FindEM ourselves, perhaps we should recommend downloading the MRC image2010 libraries compile those and then compile the single findem.f90 file against the libraries. We cannot do what we were doing without permission from the MRC/CCP4 group.
Updated by Scott Stagg about 9 years ago
I had already tried just doing 'make' and got a massive string of errors like the one you originally listed above. Below is the output from make:
./ifftlib.a(ifftsub.o): In function `odfft_': ifftsub.for:(.text+0x291): undefined reference to `s_wsfe' ifftsub.for:(.text+0x2a5): undefined reference to `do_fio' ifftsub.for:(.text+0x2ac): undefined reference to `e_wsfe' ifftsub.for:(.text+0x2ba): undefined reference to `s_stop' ./ifftlib.a(ifftsub.o): In function `todfft_': ifftsub.for:(.text+0x538): undefined reference to `s_wsfe' ifftsub.for:(.text+0x54c): undefined reference to `do_fio' ifftsub.for:(.text+0x553): undefined reference to `e_wsfe' ifftsub.for:(.text+0x561): undefined reference to `s_stop' ./ifftlib.a(ifftsub.o): In function `bigfft_': ifftsub.for:(.text+0x731): undefined reference to `s_wsfe' ifftsub.for:(.text+0x74a): undefined reference to `do_fio' ifftsub.for:(.text+0x763): undefined reference to `do_fio' ifftsub.for:(.text+0x77c): undefined reference to `do_fio' ifftsub.for:(.text+0x795): undefined reference to `do_fio' ifftsub.for:(.text+0x79c): undefined reference to `e_wsfe' ifftsub.for:(.text+0x88b): undefined reference to `s_wsfe' ifftsub.for:(.text+0x8a4): undefined reference to `do_fio' ifftsub.for:(.text+0x8bd): undefined reference to `do_fio' ifftsub.for:(.text+0x8d6): undefined reference to `do_fio' ifftsub.for:(.text+0x8ef): undefined reference to `do_fio' ifftsub.for:(.text+0x8f6): undefined reference to `e_wsfe' ifftsub.for:(.text+0xe14): undefined reference to `c_abs' ifftsub.for:(.text+0xeb4): undefined reference to `s_wsfe' ifftsub.for:(.text+0xebb): undefined reference to `e_wsfe' ifftsub.for:(.text+0xef3): undefined reference to `s_stop' ./ifftlib.a(ifftsub.o): In function `giantfft_': ifftsub.for:(.text+0x10aa): undefined reference to `s_wsfe' ifftsub.for:(.text+0x10b1): undefined reference to `e_wsfe' ifftsub.for:(.text+0x10bd): undefined reference to `s_wsfe' ifftsub.for:(.text+0x10c4): undefined reference to `e_wsfe' ifftsub.for:(.text+0x11d7): undefined reference to `s_wsfe' ifftsub.for:(.text+0x11f0): undefined reference to `do_fio' ifftsub.for:(.text+0x1209): undefined reference to `do_fio' ifftsub.for:(.text+0x1222): undefined reference to `do_fio' ifftsub.for:(.text+0x123b): undefined reference to `do_fio' ifftsub.for:(.text+0x1242): undefined reference to `e_wsfe' ifftsub.for:(.text+0x1487): undefined reference to `s_wsfe' ifftsub.for:(.text+0x14a0): undefined reference to `do_fio' ifftsub.for:(.text+0x14b9): undefined reference to `do_fio' ifftsub.for:(.text+0x14d2): undefined reference to `do_fio' ifftsub.for:(.text+0x14eb): undefined reference to `do_fio' ifftsub.for:(.text+0x14f2): undefined reference to `e_wsfe' ifftsub.for:(.text+0x16d4): undefined reference to `s_wsfe' ifftsub.for:(.text+0x16ed): undefined reference to `do_fio' ifftsub.for:(.text+0x16f4): undefined reference to `e_wsfe' ifftsub.for:(.text+0x184d): undefined reference to `s_wsfe' ifftsub.for:(.text+0x1866): undefined reference to `do_fio' ifftsub.for:(.text+0x186d): undefined reference to `e_wsfe' ifftsub.for:(.text+0x189c): undefined reference to `s_stop' ifftsub.for:(.text+0x1b6e): undefined reference to `s_wsfe' ifftsub.for:(.text+0x1b87): undefined reference to `do_fio' ifftsub.for:(.text+0x1b8e): undefined reference to `e_wsfe' ifftsub.for:(.text+0x2192): undefined reference to `s_wsfe' ifftsub.for:(.text+0x21ab): undefined reference to `do_fio' ifftsub.for:(.text+0x21b2): undefined reference to `e_wsfe' ifftsub.for:(.text+0x21e7): undefined reference to `s_wsfe' ifftsub.for:(.text+0x2200): undefined reference to `do_fio' ifftsub.for:(.text+0x2207): undefined reference to `e_wsfe' ifftsub.for:(.text+0x235c): undefined reference to `s_wsfe' ifftsub.for:(.text+0x2375): undefined reference to `do_fio' ifftsub.for:(.text+0x237c): undefined reference to `e_wsfe' ifftsub.for:(.text+0x23c2): undefined reference to `s_wsfe' ifftsub.for:(.text+0x23c9): undefined reference to `e_wsfe' ifftsub.for:(.text+0x2444): undefined reference to `s_wsfe' ifftsub.for:(.text+0x245d): undefined reference to `do_fio' ifftsub.for:(.text+0x2464): undefined reference to `e_wsfe' ifftsub.for:(.text+0x251b): undefined reference to `c_abs' ifftsub.for:(.text+0x2592): undefined reference to `s_wsfe' ifftsub.for:(.text+0x25ab): undefined reference to `do_fio' ifftsub.for:(.text+0x25b2): undefined reference to `e_wsfe' ifftsub.for:(.text+0x267e): undefined reference to `s_wsfe' ifftsub.for:(.text+0x2697): undefined reference to `do_fio' ifftsub.for:(.text+0x269e): undefined reference to `e_wsfe' ifftsub.for:(.text+0x27a2): undefined reference to `s_wsfe' ifftsub.for:(.text+0x27bb): undefined reference to `do_fio' ifftsub.for:(.text+0x27c2): undefined reference to `e_wsfe' ./ifftlib.a(ifftsub.o): In function `rsymft_': ifftsub.for:(.text+0x3801): undefined reference to `s_wsfe' ifftsub.for:(.text+0x381a): undefined reference to `do_fio' ifftsub.for:(.text+0x3821): undefined reference to `e_wsfe' ifftsub.for:(.text+0x382f): undefined reference to `s_stop' ./ifftlib.a(ifftsub.o): In function `sdiad_': ifftsub.for:(.text+0x3d81): undefined reference to `s_wsfe' ifftsub.for:(.text+0x3d97): undefined reference to `do_fio' ifftsub.for:(.text+0x3d9e): undefined reference to `e_wsfe' ifftsub.for:(.text+0x3dac): undefined reference to `s_stop' ./ifftlib.a(ifftsub.o): In function `srfp_': ifftsub.for:(.text+0x4521): undefined reference to `s_wsfe' ifftsub.for:(.text+0x4535): undefined reference to `do_fio' ifftsub.for:(.text+0x4549): undefined reference to `do_fio' ifftsub.for:(.text+0x4550): undefined reference to `e_wsfe' ifftsub.for:(.text+0x46ff): undefined reference to `s_wsfe' ifftsub.for:(.text+0x4715): undefined reference to `do_fio' ifftsub.for:(.text+0x4729): undefined reference to `do_fio' ifftsub.for:(.text+0x4730): undefined reference to `e_wsfe' ./ifftlib.a(ifftsub.o): In function `mdftkd_': ifftsub.for:(.text+0x507d): undefined reference to `s_wsfe' ifftsub.for:(.text+0x5084): undefined reference to `e_wsfe' ./ifftlib.a(ifftsub.o): In function `cmplft_': ifftsub.for:(.text+0x8218): undefined reference to `s_wsfe' ifftsub.for:(.text+0x822c): undefined reference to `do_fio' ifftsub.for:(.text+0x8233): undefined reference to `e_wsfe' ifftsub.for:(.text+0x8241): undefined reference to `s_stop' ./genlib.a(diskio.o): In function `qqopen_': diskio.for:(.text+0x4d): undefined reference to `s_copy' diskio.for:(.text+0x84): undefined reference to `s_copy' diskio.for:(.text+0x9a): undefined reference to `s_copy' diskio.for:(.text+0xb3): undefined reference to `s_cmp' diskio.for:(.text+0xeb): undefined reference to `s_cmp' diskio.for:(.text+0x114): undefined reference to `s_cmp' diskio.for:(.text+0x1a7): undefined reference to `s_wsfi' diskio.for:(.text+0x1bd): undefined reference to `do_fio' diskio.for:(.text+0x1d1): undefined reference to `do_fio' diskio.for:(.text+0x1d8): undefined reference to `e_wsfi' diskio.for:(.text+0x23c): undefined reference to `s_cat' diskio.for:(.text+0x294): undefined reference to `s_copy' diskio.for:(.text+0x2c3): undefined reference to `s_copy' diskio.for:(.text+0x2f5): undefined reference to `s_cmp' diskio.for:(.text+0x32c): undefined reference to `s_copy' diskio.for:(.text+0x348): undefined reference to `s_copy' diskio.for:(.text+0x373): undefined reference to `s_copy' diskio.for:(.text+0x3a1): undefined reference to `s_copy' diskio.for:(.text+0x3ff): undefined reference to `s_cat' diskio.for:(.text+0x430): undefined reference to `s_copy' diskio.for:(.text+0x4a1): undefined reference to `s_cmp' ./genlib.a(diskio.o): In function `qqinq_': diskio.for:(.text+0x51c): undefined reference to `s_copy' diskio.for:(.text+0x530): undefined reference to `s_copy' diskio.for:(.text+0x549): undefined reference to `s_cmp' diskio.for:(.text+0x581): undefined reference to `s_cmp' diskio.for:(.text+0x5b6): undefined reference to `s_copy' diskio.for:(.text+0x605): undefined reference to `s_copy' diskio.for:(.text+0x621): undefined reference to `s_copy' ./genlib.a(diskio.o): In function `qopen_': diskio.for:(.text+0x729): undefined reference to `s_copy' diskio.for:(.text+0x773): undefined reference to `s_cat' ./genlib.a(subs.o): In function `numchars_': subs.for:(.text+0x98): undefined reference to `s_copy' subs.for:(.text+0xc3): undefined reference to `s_cmp' subs.for:(.text+0xe0): undefined reference to `s_cmp' ./genlib.a(unix.o): In function `ccpopn_': unix.for:(.text+0x8b): undefined reference to `s_wsfe' unix.for:(.text+0x92): undefined reference to `e_wsfe' unix.for:(.text+0x10b): undefined reference to `s_cmp' unix.for:(.text+0x127): undefined reference to `s_cmp' unix.for:(.text+0x148): undefined reference to `s_cmp' unix.for:(.text+0x19a): undefined reference to `s_cmp' unix.for:(.text+0x1c0): undefined reference to `s_cmp' ./genlib.a(unix.o):unix.for:(.text+0x1e2): more undefined references to `s_cmp' follow ./genlib.a(unix.o): In function `ccpopn_': unix.for:(.text+0x204): undefined reference to `s_copy' unix.for:(.text+0x222): undefined reference to `s_cmp' unix.for:(.text+0x265): undefined reference to `s_copy' unix.for:(.text+0x29e): undefined reference to `s_copy' unix.for:(.text+0x2cd): undefined reference to `s_copy' unix.for:(.text+0x2f3): undefined reference to `s_copy' unix.for:(.text+0x30c): undefined reference to `s_cmp' unix.for:(.text+0x33d): undefined reference to `s_copy' unix.for:(.text+0x35b): undefined reference to `s_cmp' unix.for:(.text+0x3b3): undefined reference to `f_open' unix.for:(.text+0x3f0): undefined reference to `s_wsfi' unix.for:(.text+0x409): undefined reference to `do_fio' unix.for:(.text+0x422): undefined reference to `do_fio' unix.for:(.text+0x438): undefined reference to `do_fio' unix.for:(.text+0x43f): undefined reference to `e_wsfi' unix.for:(.text+0x482): undefined reference to `s_copy' unix.for:(.text+0x49a): undefined reference to `s_copy' unix.for:(.text+0x504): undefined reference to `s_cat' unix.for:(.text+0x60d): undefined reference to `s_wsfe' unix.for:(.text+0x623): undefined reference to `do_fio' unix.for:(.text+0x64d): undefined reference to `do_fio' unix.for:(.text+0x674): undefined reference to `do_fio' unix.for:(.text+0x67b): undefined reference to `e_wsfe' unix.for:(.text+0x6b3): undefined reference to `s_cat' unix.for:(.text+0x6fc): undefined reference to `s_copy' unix.for:(.text+0x741): undefined reference to `s_cmp' unix.for:(.text+0x7ca): undefined reference to `s_copy' unix.for:(.text+0x801): undefined reference to `s_copy' unix.for:(.text+0x837): undefined reference to `s_cmp' unix.for:(.text+0x864): undefined reference to `s_copy' unix.for:(.text+0x88b): undefined reference to `s_wsfe' unix.for:(.text+0x8a4): undefined reference to `do_fio' unix.for:(.text+0x8bd): undefined reference to `do_fio' unix.for:(.text+0x8d3): undefined reference to `do_fio' unix.for:(.text+0x8f2): undefined reference to `do_fio' unix.for:(.text+0x91c): undefined reference to `do_fio' ./genlib.a(unix.o):unix.for:(.text+0x93c): more undefined references to `do_fio' follow ./genlib.a(unix.o): In function `ccpopn_': unix.for:(.text+0x984): undefined reference to `f_open' unix.for:(.text+0xa41): undefined reference to `s_cat' unix.for:(.text+0xa72): undefined reference to `s_copy' ./genlib.a(unix.o): In function `__g77_masterfun_getelapsed': unix.for:(.text+0xab0): undefined reference to `G77_etime_0' unix.for:(.text+0xb0f): undefined reference to `s_wsfe' unix.for:(.text+0xb25): undefined reference to `do_fio' unix.for:(.text+0xb3b): undefined reference to `do_fio' unix.for:(.text+0xb78): undefined reference to `do_fio' unix.for:(.text+0xbbd): undefined reference to `do_fio' unix.for:(.text+0xbc4): undefined reference to `e_wsfe' ./genlib.a(unix.o): In function `ttsend_': unix.for:(.text+0xc2e): undefined reference to `s_copy' unix.for:(.text+0xc47): undefined reference to `s_cmp' unix.for:(.text+0xca9): undefined reference to `s_wsfe' unix.for:(.text+0xcbb): undefined reference to `do_fio' unix.for:(.text+0xcc2): undefined reference to `e_wsfe' ./genlib.a(unix.o): In function `hciftime_': unix.for:(.text+0x109f): undefined reference to `s_wsle' unix.for:(.text+0x10ba): undefined reference to `do_lio' unix.for:(.text+0x10c1): undefined reference to `e_wsle' unix.for:(.text+0x10d7): undefined reference to `s_copy' unix.for:(.text+0x10f3): undefined reference to `G77_time_0' unix.for:(.text+0x1108): undefined reference to `G77_gmtime_0' unix.for:(.text+0x1119): undefined reference to `G77_ltime_0' unix.for:(.text+0x120c): undefined reference to `s_wsfi' unix.for:(.text+0x1222): undefined reference to `do_fio' unix.for:(.text+0x1238): undefined reference to `do_fio' unix.for:(.text+0x124e): undefined reference to `do_fio' unix.for:(.text+0x1264): undefined reference to `do_fio' unix.for:(.text+0x127a): undefined reference to `do_fio' ./genlib.a(unix.o):unix.for:(.text+0x1290): more undefined references to `do_fio' follow ./genlib.a(unix.o): In function `hciftime_': unix.for:(.text+0x12ef): undefined reference to `e_wsfi' ./genlib.a(unix.o): In function `ugerr_': unix.for:(.text+0x1348): undefined reference to `ierrno_' unix.for:(.text+0x1358): undefined reference to `G77_gerror_0' unix.for:(.text+0x1386): undefined reference to `s_copy' unix.for:(.text+0x13a9): undefined reference to `s_wsfe' unix.for:(.text+0x13bf): undefined reference to `do_fio' unix.for:(.text+0x13d0): undefined reference to `do_fio' ./genlib.a(unix.o): In function `ustime_': unix.for:(.text+0x1487): undefined reference to `G77_time_0' ./genlib.a(unix.o): In function `ucputm_': unix.for:(.text+0x14c8): undefined reference to `G77_etime_0' unix.for:(.text+0x14f0): undefined reference to `G77_etime_0' ./genlib.a(unix.o): In function `ugtuid_': unix.for:(.text+0x1535): undefined reference to `G77_getenv_0' unix.for:(.text+0x154b): undefined reference to `s_cmp' ./genlib.a(unix.o): In function `uidate_': unix.for:(.text+0x15b2): undefined reference to `G77_idate_0' ./genlib.a(unix.o): In function `uisatt_': unix.for:(.text+0x15ed): undefined reference to `isatty_' ./genlib.a(unix.o): In function `utime_': unix.for:(.text+0x161f): undefined reference to `G77_itime_0' unix.for:(.text+0x1639): undefined reference to `s_wsfi' unix.for:(.text+0x164d): undefined reference to `do_fio' unix.for:(.text+0x1663): undefined reference to `do_fio' unix.for:(.text+0x1679): undefined reference to `do_fio' unix.for:(.text+0x1680): undefined reference to `e_wsfi' ./genlib.a(unix.o): In function `cexit_': unix.for:(.text+0x16e7): undefined reference to `G77_exit_0' ./genlib.a(unix.o): In function `ugerr_': unix.for:(.text+0x13e9): undefined reference to `e_wsfe' ./genlib.a(unix.o): In function `ugtenv_': unix.for:(.text+0x1443): undefined reference to `G77_getenv_0' ./genlib.a(unix.o): In function `ubytes_': unix.for:(.text+0x146e): undefined reference to `s_copy' ./genlib.a(unix.o): In function `ugtuid_': unix.for:(.text+0x1580): undefined reference to `G77_getenv_0' ./genlib.a(unix.o): In function `ugtarg_': unix.for:(.text+0x16c3): undefined reference to `G77_getarg_0' ./genlib.a(unix.o): In function `ccpspw_': unix.for:(.text+0x16d3): undefined reference to `system_' ./genlib.a(ccplib.o): In function `ccpale_': ccplib.for:(.text+0x106): undefined reference to `i_indx' ccplib.for:(.text+0x15c): undefined reference to `s_cat' ccplib.for:(.text+0x21d): undefined reference to `s_wsfe' ccplib.for:(.text+0x224): undefined reference to `e_wsfe' ccplib.for:(.text+0x242): undefined reference to `s_wsfe' ccplib.for:(.text+0x27f): undefined reference to `do_fio' ccplib.for:(.text+0x295): undefined reference to `do_fio' ccplib.for:(.text+0x2ae): undefined reference to `do_fio' ccplib.for:(.text+0x2b9): undefined reference to `e_wsfe' ./genlib.a(ccplib.o): In function `ccpdpn_': ccplib.for:(.text+0x58b): undefined reference to `s_copy' ccplib.for:(.text+0x5a4): undefined reference to `s_copy' ccplib.for:(.text+0x5f1): undefined reference to `s_cmp' ccplib.for:(.text+0x61b): undefined reference to `s_copy' ccplib.for:(.text+0x648): undefined reference to `s_copy' ccplib.for:(.text+0x68f): undefined reference to `s_cmp' ccplib.for:(.text+0x6b9): undefined reference to `s_copy' ccplib.for:(.text+0x6e8): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccpe2i_': ccplib.for:(.text+0x7da): undefined reference to `s_cmp' ccplib.for:(.text+0x82f): undefined reference to `s_rsfi' ccplib.for:(.text+0x85a): undefined reference to `s_copy' ccplib.for:(.text+0x89b): undefined reference to `s_copy' ccplib.for:(.text+0x8e0): undefined reference to `do_fio' ccplib.for:(.text+0x8ed): undefined reference to `e_rsfi' ccplib.for:(.text+0x930): undefined reference to `s_copy' ccplib.for:(.text+0x987): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccperr_': ccplib.for:(.text+0x9f6): undefined reference to `s_copy' ccplib.for:(.text+0xa8c): undefined reference to `s_cat' ccplib.for:(.text+0xb55): undefined reference to `s_copy' ccplib.for:(.text+0xbc1): undefined reference to `s_cmp' ccplib.for:(.text+0xc98): undefined reference to `s_cmp' ccplib.for:(.text+0xcde): undefined reference to `s_wsle' ccplib.for:(.text+0xcf7): undefined reference to `do_lio' ccplib.for:(.text+0xcfe): undefined reference to `e_wsle' ./genlib.a(ccplib.o): In function `ccpfyp_': ccplib.for:(.text+0xd67): undefined reference to `f__xargc' ccplib.for:(.text+0xe71): undefined reference to `s_cmp' ccplib.for:(.text+0xe99): undefined reference to `s_cmp' ccplib.for:(.text+0xec5): undefined reference to `s_cmp' ccplib.for:(.text+0xf8f): undefined reference to `s_cmp' ccplib.for:(.text+0xfd0): undefined reference to `s_copy' ccplib.for:(.text+0x1037): undefined reference to `s_cat' ccplib.for:(.text+0x10c4): undefined reference to `s_rsfe' ccplib.for:(.text+0x10fd): undefined reference to `s_copy' ccplib.for:(.text+0x1118): undefined reference to `i_indx' ccplib.for:(.text+0x1141): undefined reference to `i_indx' ccplib.for:(.text+0x116a): undefined reference to `s_cmp' ccplib.for:(.text+0x11b7): undefined reference to `i_indx' ccplib.for:(.text+0x11fe): undefined reference to `s_copy' ccplib.for:(.text+0x1266): undefined reference to `s_cat' ccplib.for:(.text+0x128b): undefined reference to `s_cmp' ccplib.for:(.text+0x12b8): undefined reference to `i_indx' ccplib.for:(.text+0x12ef): undefined reference to `s_copy' ccplib.for:(.text+0x1307): undefined reference to `s_rsfe' ccplib.for:(.text+0x1329): undefined reference to `do_fio' ccplib.for:(.text+0x133c): undefined reference to `e_rsfe' ccplib.for:(.text+0x1364): undefined reference to `f_clos' ccplib.for:(.text+0x13c8): undefined reference to `s_cmp' ccplib.for:(.text+0x1428): undefined reference to `s_copy' ccplib.for:(.text+0x1467): undefined reference to `s_cat' ccplib.for:(.text+0x14f6): undefined reference to `s_rsfe' ccplib.for:(.text+0x152d): undefined reference to `s_copy' ccplib.for:(.text+0x1548): undefined reference to `i_indx' ccplib.for:(.text+0x1571): undefined reference to `i_indx' ccplib.for:(.text+0x159a): undefined reference to `s_cmp' ccplib.for:(.text+0x15bd): undefined reference to `i_indx' ccplib.for:(.text+0x15e9): undefined reference to `s_copy' ccplib.for:(.text+0x1616): undefined reference to `s_copy' ccplib.for:(.text+0x1687): undefined reference to `s_rsfe' ccplib.for:(.text+0x16a9): undefined reference to `do_fio' ccplib.for:(.text+0x16bc): undefined reference to `e_rsfe' ccplib.for:(.text+0x16e2): undefined reference to `f_clos' ccplib.for:(.text+0x17f8): undefined reference to `s_cmp' ccplib.for:(.text+0x1888): undefined reference to `s_cmp' ccplib.for:(.text+0x18fb): undefined reference to `s_copy' ccplib.for:(.text+0x1922): undefined reference to `s_copy' ccplib.for:(.text+0x1949): undefined reference to `s_copy' ccplib.for:(.text+0x1970): undefined reference to `s_copy' ccplib.for:(.text+0x19d6): undefined reference to `s_cat' ccplib.for:(.text+0x1a3a): undefined reference to `s_cat' ccplib.for:(.text+0x1aa6): undefined reference to `s_cat' ccplib.for:(.text+0x1ae3): undefined reference to `s_cmp' ccplib.for:(.text+0x1b80): undefined reference to `s_cat' ccplib.for:(.text+0x1c58): undefined reference to `s_cat' ccplib.for:(.text+0x1d0c): undefined reference to `s_cmp' ccplib.for:(.text+0x1d66): undefined reference to `s_cmp' ccplib.for:(.text+0x1dac): undefined reference to `s_copy' ccplib.for:(.text+0x1ded): undefined reference to `s_cmp' ccplib.for:(.text+0x1e49): undefined reference to `s_cmp' ccplib.for:(.text+0x1e8f): undefined reference to `s_copy' ccplib.for:(.text+0x1ee8): undefined reference to `s_cmp' ccplib.for:(.text+0x1f42): undefined reference to `s_cmp' ccplib.for:(.text+0x1f84): undefined reference to `s_copy' ccplib.for:(.text+0x1fc5): undefined reference to `s_cmp' ccplib.for:(.text+0x2023): undefined reference to `s_cmp' ccplib.for:(.text+0x206d): undefined reference to `s_copy' ccplib.for:(.text+0x20fc): undefined reference to `s_cmp' ccplib.for:(.text+0x2176): undefined reference to `s_cmp' ccplib.for:(.text+0x21d9): undefined reference to `s_copy' ccplib.for:(.text+0x2210): undefined reference to `s_copy' ccplib.for:(.text+0x2262): undefined reference to `s_cmp' ccplib.for:(.text+0x22dc): undefined reference to `s_cmp' ccplib.for:(.text+0x233f): undefined reference to `s_copy' ccplib.for:(.text+0x2376): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccppsf_': ccplib.for:(.text+0x24da): undefined reference to `s_copy' ccplib.for:(.text+0x24f4): undefined reference to `s_copy' ccplib.for:(.text+0x250e): undefined reference to `s_copy' ./genlib.a(ccplib.o):ccplib.for:(.text+0x2528): more undefined references to `s_copy' follow ./genlib.a(ccplib.o): In function `ccppsf_': ccplib.for:(.text+0x25a4): undefined reference to `s_cmp' ccplib.for:(.text+0x25e2): undefined reference to `s_cmp' ccplib.for:(.text+0x2603): undefined reference to `s_cmp' ccplib.for:(.text+0x264f): undefined reference to `s_cmp' ccplib.for:(.text+0x267c): undefined reference to `s_copy' ccplib.for:(.text+0x26c4): undefined reference to `s_cmp' ccplib.for:(.text+0x26ed): undefined reference to `s_copy' ccplib.for:(.text+0x2734): undefined reference to `s_cmp' ccplib.for:(.text+0x275b): undefined reference to `i_indx' ccplib.for:(.text+0x2797): undefined reference to `s_copy' ccplib.for:(.text+0x2815): undefined reference to `s_cmp' ccplib.for:(.text+0x2872): undefined reference to `s_copy' ccplib.for:(.text+0x2897): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccprcs_': ccplib.for:(.text+0x28e1): undefined reference to `s_cmp' ccplib.for:(.text+0x2909): undefined reference to `s_copy' ccplib.for:(.text+0x295b): undefined reference to `s_cmp' ccplib.for:(.text+0x2978): undefined reference to `s_cmp' ccplib.for:(.text+0x29a0): undefined reference to `s_copy' ccplib.for:(.text+0x29ba): undefined reference to `s_copy' ccplib.for:(.text+0x29d3): undefined reference to `s_copy' ccplib.for:(.text+0x29fa): undefined reference to `s_copy' ccplib.for:(.text+0x2a14): undefined reference to `s_copy' ./genlib.a(ccplib.o):ccplib.for:(.text+0x2a2d): more undefined references to `s_copy' follow ./genlib.a(ccplib.o): In function `csetnv_': ccplib.for:(.text+0x2ac1): undefined reference to `s_cmp' ccplib.for:(.text+0x2b26): undefined reference to `s_cmp' ccplib.for:(.text+0x2b7d): undefined reference to `s_cmp' ccplib.for:(.text+0x2baa): undefined reference to `s_copy' ccplib.for:(.text+0x2bc4): undefined reference to `s_copy' ccplib.for:(.text+0x2c16): undefined reference to `s_copy' ccplib.for:(.text+0x2c3e): undefined reference to `s_copy' ccplib.for:(.text+0x2c75): undefined reference to `s_copy' ccplib.for:(.text+0x2cb5): undefined reference to `s_cmp' ccplib.for:(.text+0x2cd2): undefined reference to `s_cmp' ccplib.for:(.text+0x2d05): undefined reference to `s_cmp' ccplib.for:(.text+0x2d46): undefined reference to `s_copy' ccplib.for:(.text+0x2d6a): undefined reference to `s_copy' ccplib.for:(.text+0x2d9a): undefined reference to `s_copy' ccplib.for:(.text+0x2df5): undefined reference to `s_copy' ccplib.for:(.text+0x2e0f): undefined reference to `s_copy' ccplib.for:(.text+0x2e64): undefined reference to `s_cmp' ccplib.for:(.text+0x2eac): undefined reference to `s_copy' ccplib.for:(.text+0x2eda): undefined reference to `s_cmp' ccplib.for:(.text+0x2f16): undefined reference to `s_copy' ccplib.for:(.text+0x2f56): undefined reference to `i_indx' ccplib.for:(.text+0x2f78): undefined reference to `s_copy' ccplib.for:(.text+0x2fc8): undefined reference to `s_copy' ccplib.for:(.text+0x301b): undefined reference to `s_cmp' ccplib.for:(.text+0x303a): undefined reference to `s_cmp' ccplib.for:(.text+0x3094): undefined reference to `s_cmp' ccplib.for:(.text+0x3109): undefined reference to `s_cat' ccplib.for:(.text+0x313a): undefined reference to `s_copy' ccplib.for:(.text+0x3151): undefined reference to `s_copy' ccplib.for:(.text+0x317b): undefined reference to `f_inqu' ccplib.for:(.text+0x31a6): undefined reference to `s_copy' ccplib.for:(.text+0x31bf): undefined reference to `s_copy' ccplib.for:(.text+0x31f5): undefined reference to `s_cmp' ccplib.for:(.text+0x3273): undefined reference to `s_cmp' ccplib.for:(.text+0x3296): undefined reference to `s_cmp' ccplib.for:(.text+0x32c5): undefined reference to `s_cmp' ccplib.for:(.text+0x32fc): undefined reference to `s_cmp' ./genlib.a(ccplib.o):ccplib.for:(.text+0x3358): more undefined references to `s_cmp' follow ./genlib.a(ccplib.o): In function `csetnv_': ccplib.for:(.text+0x33e8): undefined reference to `s_cat' ccplib.for:(.text+0x3420): undefined reference to `s_copy' ccplib.for:(.text+0x343d): undefined reference to `i_indx' ccplib.for:(.text+0x3464): undefined reference to `s_copy' ccplib.for:(.text+0x3489): undefined reference to `s_wsfi' ccplib.for:(.text+0x3490): undefined reference to `getpid_' ccplib.for:(.text+0x34aa): undefined reference to `do_fio' ccplib.for:(.text+0x34b1): undefined reference to `e_wsfi' ccplib.for:(.text+0x352a): undefined reference to `s_cat' ccplib.for:(.text+0x354a): undefined reference to `s_cmp' ccplib.for:(.text+0x3569): undefined reference to `s_copy' ccplib.for:(.text+0x35ce): undefined reference to `getpid_' ccplib.for:(.text+0x360e): undefined reference to `s_wsfi' ccplib.for:(.text+0x3638): undefined reference to `s_cmp' ccplib.for:(.text+0x36c2): undefined reference to `s_cat' ccplib.for:(.text+0x36f2): undefined reference to `s_cmp' ccplib.for:(.text+0x370f): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `__g77_masterfun_ccpvrs': ccplib.for:(.text+0x37d4): undefined reference to `s_copy' ccplib.for:(.text+0x37ef): undefined reference to `s_copy' ccplib.for:(.text+0x385b): undefined reference to `s_wsfi' ccplib.for:(.text+0x3871): undefined reference to `do_fio' ccplib.for:(.text+0x3887): undefined reference to `do_fio' ccplib.for:(.text+0x389d): undefined reference to `do_fio' ccplib.for:(.text+0x38a4): undefined reference to `e_wsfi' ccplib.for:(.text+0x38f5): undefined reference to `s_copy' ccplib.for:(.text+0x390a): undefined reference to `s_wsfe' ccplib.for:(.text+0x3920): undefined reference to `do_fio' ccplib.for:(.text+0x3940): undefined reference to `do_fio' ccplib.for:(.text+0x3954): undefined reference to `do_fio' ccplib.for:(.text+0x3974): undefined reference to `do_fio' ccplib.for:(.text+0x3988): undefined reference to `do_fio' ./genlib.a(ccplib.o):ccplib.for:(.text+0x399e): more undefined references to `do_fio' follow ./genlib.a(ccplib.o): In function `__g77_masterfun_ccpvrs': ccplib.for:(.text+0x39a5): undefined reference to `e_wsfe' ccplib.for:(.text+0x39d7): undefined reference to `s_cmp' ccplib.for:(.text+0x39f3): undefined reference to `s_copy' ccplib.for:(.text+0x3a4f): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `__g77_masterfun_qprint': ccplib.for:(.text+0x3aad): undefined reference to `s_cmp' ccplib.for:(.text+0x3ae8): undefined reference to `s_wsfe' ccplib.for:(.text+0x3b03): undefined reference to `do_fio' ccplib.for:(.text+0x3b0a): undefined reference to `e_wsfe' ccplib.for:(.text+0x3b60): undefined reference to `s_wsfe' ccplib.for:(.text+0x3b87): undefined reference to `s_wsfe' ccplib.for:(.text+0x3b98): undefined reference to `do_fio' ./genlib.a(ccplib.o): In function `ccpalc_': ccplib.for:(.text+0x3c36): undefined reference to `i_indx' ccplib.for:(.text+0x3cf1): undefined reference to `s_cat' ./genlib.a(ccplib.o): In function `ccpupc_': ccplib.for:(.text+0x3d7d): undefined reference to `i_indx' ccplib.for:(.text+0x3db4): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccpdat_': ccplib.for:(.text+0x3ee7): undefined reference to `s_wsfi' ccplib.for:(.text+0x3efd): undefined reference to `do_fio' ccplib.for:(.text+0x3f13): undefined reference to `do_fio' ccplib.for:(.text+0x3f29): undefined reference to `do_fio' ccplib.for:(.text+0x3f30): undefined reference to `e_wsfi' ./genlib.a(ccplib.o): In function `ccpexs_': ccplib.for:(.text+0x4015): undefined reference to `s_copy' ccplib.for:(.text+0x4042): undefined reference to `s_cmp' ccplib.for:(.text+0x4065): undefined reference to `f_inqu' ccplib.for:(.text+0x409e): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccplwc_': ccplib.for:(.text+0x44cd): undefined reference to `i_indx' ccplib.for:(.text+0x4504): undefined reference to `s_copy' ./genlib.a(ccplib.o): In function `ccpnun_': ccplib.for:(.text+0x4602): undefined reference to `f_inqu' ./genlib.a(ccplib.o): In function `lenstr_': ccplib.for:(.text+0x4c6a): undefined reference to `s_cmp' ./genlib.a(ccplib.o): In function `__g77_masterfun_qprint': ccplib.for:(.text+0x3b71): undefined reference to `e_wsfe' ./genlib.a(ccplib.o): In function `ccp4_version_': ccplib.for:(.text+0x4a8f): undefined reference to `s_copy' /usr/bin/ld: link errors found, deleting executab
Updated by Scott Stagg about 9 years ago
I tried downloading imag2010 and copying all the .a files from 'lib' into the appion findem directory then recompiling. It compiled with no errors, but when I tried 'make test' or manually testing, I get this error:
Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7F572ED0F467 #1 0x7F572ED0FAAE #2 0x7F572E21664F #3 0x41FC25 in qseek_ #4 0x41729D in master.0.imopen_ at imsubs2000.for:? #5 0x417778 in imopen_ #6 0x40AA62 in MAIN__ at findem.f90:? Segmentation fault
Updated by Neil Voss about 9 years ago
- Assignee changed from Neil Voss to Anchi Cheng
Hi Anchi, apparently the new image2010 package has trouble reading MRCs created using pyami. Do you know anything about this? I am unsure if this is related to Scott's segfault, but this is what I get.
Has something changed with the MRC format? I am not sure how to proceed. Maybe we'll have to switch to findEM2 or implement the code in python.
vosslab@fourier findem] make test
rm -fv cccmaxmap001.mrc
./findem64.exe < feedtest.txt
X Fast FindEM Program:
>>> enter filename of the image file :
X ... image: 07jan05b_12gr_02en_00.dwn2.mrc
>>> enter filename of the search template :
X ... template: grostain3.dwn2.mrc
>>> (for backward compat) enter any random float 0,1 :
>>> enter pixelsize of the images in angstroms/pixel :
X ... A/pix: 22.7999992
>>> enter a diameter of particles (a)
X ... part diam: 140.000000
>>> enter a runcode
X ... runcode: 1
>>> enter angle start, limit, stepsize
X ... angles: 0.00000000 179.000000 20.0000000
>>> enter border size
X ... border: 50
>>>>>> CCP4 library signal library_file:End of File (Error)
raised in ccp4_file_raw_read <<<<<<
>>>>>> System signal 2:No such file or directory (Error)
raised in ccp4_file_readfloat <<<<<<
STOP error on file read1.
Updated by Anchi Cheng about 9 years ago
mrc package has a header.exe that reads and prints header of the mrc file. If you can run that on the file, that may tell us something. The current pyam/mrc.py should be compatible to mrc2010 (at least what we agreed) if there is no extended header involve.
this tempplate file is a 2D image, not an image stack, right ?
Updated by Neil Voss about 9 years ago
I tried creating new MRC with trunk pyami and it still gives the same error. I will think more about it, but since the code is FORTRAN it is a tough thing to debug for me.
Updated by Neil Voss about 9 years ago
Sorry, I did not. I was concern it would take me awhile to find it. The MRCs are in subversion. Have you tried to compile FindEM recently?
Updated by Anchi Cheng about 9 years ago
Regarding mrc file generated from pyami.mrc not readable, I tried it with a local image2010 package installation on CetOS 6. Reading the file through its standard file handling programs under bin subfolder: label.exe and Ximdisp. Both were able to read mrc files generated from pyami.mrc. The installation is built with g77 or gfortrain, though.
Updated by Anchi Cheng about 9 years ago
- Assignee changed from Anchi Cheng to Scott Stagg
I was able to debug findem.f90 and found a bug in closing an image stream that was never opened, giving segmentation error for me when I compiled with image2010 compiled library as committed as r19152. This was done on CentOS6 but the MakeFile does not use f77.
Whether this will work for you two, I don't know, though, because even without the bug fix, I don't get the readfloat error from ccp4. My compiled findem64.exe ran through the program and only got Segmentation Fault at the end which is inconsequential since needed files are written already.
Updated by Scott Stagg about 9 years ago
I tried compiling with from the findem code in the trunk and got this error:
[sstagg@imb findem]$ make gfortran -O3 -w -march=native -mtune=native -o ./findem64.exe findem.f90 ./imlib2010.a ./ifftlib.a ./genlib.a ./misclib.a ./plot2klib.a gfortran: error: ./ifftlib.a: No such file or directory gfortran: error: ./genlib.a: No such file or directory gfortran: error: ./misclib.a: No such file or directory gfortran: error: ./plot2klib.a: No such file or directory make: *** [quick] Error 1
That suggests to me that I don't have some necessary library in my path. Do I need to copy something from image2010 into my findem directory?
Updated by Anchi Cheng about 9 years ago
They are in the repository.
http://emg.nysbc.org/projects/leginon/repository/show/trunk/programs/findem
I don't know what is wrong with your sandbox. Maybe it is left at a specific revision ?
Updated by Scott Stagg about 9 years ago
I don't get it. I removed the findem directory, then svn updated, and I don't get all the files. SVN tells me I'm at revision 19174, but it's not downloading all the files from trunk.
[sstagg@imb programs]$ svn update Updating '.': Restored 'findem' Restored 'findem/07jan05b_12gr_02en_00.dwn.mrc' Restored 'findem/Makefile' Restored 'findem/oldfindem.f90' Restored 'findem/imlib2010.a' Restored 'findem/findem.f90' Restored 'findem/grostain3.dwn.mrc' Restored 'findem/feedtest.txt' Restored 'findem/original_findem.f90' Restored 'findem/library.c' Restored 'findem/library.h' At revision 19174. [sstagg@imb programs]$ cd findem/ [sstagg@imb findem]$ ls 07jan05b_12gr_02en_00.dwn.mrc imlib2010.a oldfindem.f90 feedtest.txt library.c original_findem.f90 findem.f90 library.h grostain3.dwn.mrc Makefile [sstagg@imb findem]$ [sstagg@imb findem]$ [sstagg@imb findem]$ ls 07jan05b_12gr_02en_00.dwn.mrc imlib2010.a oldfindem.f90 feedtest.txt library.c original_findem.f90 findem.f90 library.h grostain3.dwn.mrc Makefile [sstagg@imb findem]$ make gfortran -O3 -w -march=native -mtune=native -o ./findem64.exe findem.f90 ./imlib2010.a ./ifftlib.a ./genlib.a ./misclib.a ./plot2klib.a gfortran: error: ./ifftlib.a: No such file or directory gfortran: error: ./genlib.a: No such file or directory gfortran: error: ./misclib.a: No such file or directory gfortran: error: ./plot2klib.a: No such file or directory make: *** [quick] Error 1
Updated by Scott Stagg about 9 years ago
On a fresh SVN checkout, it works, but I'd still iike to figure out what is going on with my other SVN directory. That is the one that all of the FSU users use.
Updated by Clint Potter about 9 years ago
- Status changed from Assigned to Closed
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