FindEM does not work on modern OS's with newer GCC

[leginonbot]

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Author Name: Neil Voss (@vosslab) Original Redmine Issue: 3472, https://emg.nysbc.org/redmine/issues/3472 Original Date: 2015-08-31 Original Assignee: Scott Stagg

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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.

http://www.ccpem.ac.uk/download.php

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-08-31T17:12:24Z

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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

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-08-31T17:32:52Z

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As I recall, mrc library relies on ccp4 library to build. Maybe that is what is missing ?

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-08-31T17:51:01Z

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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.

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-08T21:09:38Z

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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?

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-08T21:18:14Z

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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?

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-09-08T21:55:54Z

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First, do not type 'make findem' just type 'make' and it should work.

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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.

http://www.ccpem.ac.uk/download.php

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-09T02:51:43Z

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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

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-09T04:21:05Z

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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

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-09-09T15:12:56Z

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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.

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-09T19:19:28Z

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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 ?

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-09-09T22:01:23Z

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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.

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-10T01:00:25Z

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Did you try header,exe ?

[leginonbot]

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Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2015-09-10T02:08:21Z

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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?

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-14T15:23:10Z

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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.

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-14T20:27:42Z

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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.

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-16T21:12:54Z

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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?

[leginonbot]

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Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2015-09-17T02:20:33Z

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They are in the repository.

http://emg.nysbc.org/redmine/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 ?

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-17T02:34:58Z

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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

[leginonbot]

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Original Redmine Comment Author Name: Scott Stagg (Scott Stagg) Original Date: 2015-09-17T02:39:55Z

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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.