Setting up CUDAMPF program problem core dumped

mgradowski89 · January 13, 2019, 2:56pm

Hey guys, Im green in CUDA programming , just need to setup bioinformatic program (Im biologist).
Maybe someone will help, cause I fight with this for about 3 weeks.

Here is the program

My computer/system specs:

cat /etc/issue
Ubuntu 14.04.5 LTS

$ cat /proc/driver/nvidia/gpus/0000\:01\:00.0/information 
Model: 		 GeForce GTX 960M
IRQ:   		 133
GPU UUID: 	 GPU-979fb942-e752-0554-b26a-380bec0967f5
Video BIOS: 	 82.07.82.00.10
Bus Type: 	 PCIe
DMA Size: 	 40 bits
DMA Mask: 	 0xffffffffff
Bus Location: 	 0000:01:00.0
Device Minor: 	 0

$ nvcc --version
nvcc: NVIDIA (R) Cuda compiler driver
Copyright (c) 2005-2015 NVIDIA Corporation
Built on Mon_Feb_16_22:59:02_CST_2015
Cuda compilation tools, release 7.0, V7.0.27

$ echo $PATH
/usr/local/cuda-7.0/bin:~/blast/ncbi-blast-2.2.28+-src/c++/GCC480-ReleaseMT64/bin:~/miniconda3/bin:/home/marcin/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/local/cuda/bin:/home/marcin/ffas/soft

$ echo $LD_LIBRARY_PATH
/usr/local/cuda-7.0/lib64

I have set:

echo -e "blacklist nouveau\nblacklist lbm-nouveau\noptions nouveau modeset=0\nalias nouveau off\nalias lbm-nouveau off\n" | sudo tee /etc/modprobe.d/blacklist-nouveau.conf
echo options nouveau modeset=0 | sudo tee -a /etc/modprobe.d/nouveau-kms.conf
sudo update-initramfs -u

I do installation from site instruction:

1. unpacking CUDAMPF-master.zip
2. $ cd CUDAMPF-master/one\ batchIO\ version/
3. make all

and get this:

$ make all
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o main_function.o -c main_function.cpp -I.
In file included from main_function.cpp:7:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from header_def.h:12,
                 from main_function.cpp:7:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
main_function.cpp: In function 'int main(int, char**)':
main_function.cpp:192:39: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
    handle = read_kernel("SMEM_SSV.cuh"); /* read SMEM */
                                       ^
main_function.cpp:207:39: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
    handle = read_kernel("LMEM_SSV.cuh");  /* read LMEM */
                                       ^
main_function.cpp:230:39: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
    handle = read_kernel("SMEM_MSV.cuh");
                                       ^
main_function.cpp:243:39: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
    handle = read_kernel("LMEM_MSV.cuh");
                                       ^
main_function.cpp:262:39: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
    handle = read_kernel("SMEM_VIT.cuh");
                                       ^
main_function.cpp:275:39: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
    handle = read_kernel("LMEM_VIT.cuh");
                                       ^
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o model_config.o -c model_config.cpp -I.
In file included from model_config.cpp:14:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from model_config.cpp:10:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o other_function.o -c other_function.cpp -I.
In file included from other_function.cpp:5:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from other_function.cpp:3:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o read_file.o -c read_file.cpp -I.
In file included from read_file.cpp:16:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from read_file.cpp:10:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
read_file.cpp: In function 'int get_hmm_size(char*)':
read_file.cpp:24:14: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* LEN = "LENG";
              ^
read_file.cpp: In function 'int get_Parameters(HMMER_PROFILE*, char*)':
read_file.cpp:67:14: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* LEN = "LENG";
              ^
read_file.cpp:68:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* PARA_MSV = "STATS LOCAL MSV";
                   ^
read_file.cpp:69:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* PARA_VIT = "STATS LOCAL VITERBI";
                   ^
read_file.cpp:70:19: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* PARA_FWD = "STATS LOCAL FORWARD";
                   ^
read_file.cpp: In function 'int get_Emission(HMMER_PROFILE*, char*)':
read_file.cpp:188:16: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* BEGIN = "  COMPO   ";
                ^
read_file.cpp: In function 'int get_transition(HMMER_PROFILE*, char*)':
read_file.cpp:286:16: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
  char* BEGIN = "  COMPO   ";
                ^
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o degenerate.o -c degenerate.cpp -I.
In file included from degenerate.cpp:5:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from degenerate.cpp:3:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o RTC_MSV.o -c RTC_MSV.cpp -I.
In file included from RTC_MSV.cpp:5:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from header_def.h:12,
                 from RTC_MSV.cpp:5:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
RTC_MSV.cpp: In function 'void RTC_MSV(unsigned int, const char*, HMMER_PROFILE*, unsigned int*, unsigned int*, unsigned int*, unsigned int*, unsigned int, double*, int, int, dim3, dim3)':
RTC_MSV.cpp:214:88: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  printf("| %d   | %d   | %d   |\n", n_pass_msv + pass_vit_msv, n_pass_msv, pass_vit_msv);
                                                                                        ^
RTC_MSV.cpp:214:88: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=]
RTC_MSV.cpp:214:88: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=]
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o RTC_VIT.o -c RTC_VIT.cpp -I.
In file included from RTC_VIT.cpp:5:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from header_def.h:12,
                 from RTC_VIT.cpp:5:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
RTC_VIT.cpp: In function 'void RTC_VIT(unsigned int, const char*, HMMER_PROFILE*, unsigned int*, unsigned int*, unsigned int*, unsigned int*, unsigned int, double*, int, int, dim3, dim3)':
RTC_VIT.cpp:212:49: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  printf("| %d   | %d   |\n",  pass_vit, pass_vit);
                                                 ^
RTC_VIT.cpp:212:49: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=]
g++ -I/usr/local/cuda-7.0/samples/common/inc -I/usr/local/cuda-7.0/include   -o RTC_SSV.o -c RTC_SSV.cpp -I.
In file included from RTC_SSV.cpp:5:0:
header_def.h:48:0: warning: "INFINITY" redefined [enabled by default]
 #define INFINITY       999999999                    //infinity
 ^
In file included from /usr/include/math.h:38:0,
                 from header_def.h:12,
                 from RTC_SSV.cpp:5:
/usr/include/x86_64-linux-gnu/bits/inf.h:26:0: note: this is the location of the previous definition
 # define INFINITY (__builtin_inff())
 ^
RTC_SSV.cpp: In function 'void RTC_SSV(unsigned int, const char*, HMMER_PROFILE*, unsigned int*, unsigned int*, unsigned int*, unsigned int*, unsigned int, double*, int, int, dim3, dim3)':
RTC_SSV.cpp:233:102: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long unsigned int' [-Wformat=]
  printf("| RECAL = %d   | PASS SSV = %d   | PASS VIT = %d   |\n", n_recal_msv, n_pass_ssv, n_pass_vit);
                                                                                                      ^
RTC_SSV.cpp:233:102: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long unsigned int' [-Wformat=]
RTC_SSV.cpp:233:102: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long unsigned int' [-Wformat=]
g++  -L/usr/local/cuda-7.0/lib64 -L/usr/local/cuda-7.0/lib64/stubs -o CUDAMPF main_function.o model_config.o other_function.o read_file.o degenerate.o RTC_MSV.o RTC_VIT.o RTC_SSV.o  -lcuda -lnvrtc -I.

And if i run ./CUDAMPF

Your input is: (null)
Segmentation fault (core dumped)

Masters of CUDA programming please help!

APPENDIX:
I do the same thing on my second machine with Geforce 1050ti (laptop, but i hear that this card is too CUDA capable) same system and identical problem.
EDIT:

$ nvidia-smi
Sun Jan 13 16:08:00 2019       
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 384.130                Driver Version: 384.130                   |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  GeForce GTX 960M    Off  | 00000000:01:00.0 Off |                  N/A |
| N/A   43C    P0    N/A /  N/A |    323MiB /  4044MiB |      2%      Default |
+-------------------------------+----------------------+----------------------+
                                                                               
+-----------------------------------------------------------------------------+
| Processes:                                                       GPU Memory |
|  GPU       PID   Type   Process name                             Usage      |
|=============================================================================|
|    0      1193      G   /usr/lib/xorg/Xorg                           166MiB |
|    0      2071      G   compiz                                        37MiB |
|    0      2511      G   ...quest-channel-token=5394311594019641651   117MiB |
+-----------------------------------------------------------------------------+

Robert_Crovella · January 14, 2019, 1:14am

The problem is that you are not providing proper input.

Re-read the readme and learn how to run the program correctly. It expects command-line parameters:

https://github.com/Super-Hippo/CUDAMPF

###Run code

CUDAMPF [filterOpt] [modelOpt] [databaseOpt]
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
         You must provide proper command-line entries here or you will get a seg fault

If you read that entire readme, you will see that it requires one of 3 specific command line switches for the first entry, a specific model file (name) for the second entry - and the project includes some models you can use, and the third command line parameter must be a protein database file in FASTA format, and it gives you a link where you can download such a file.

Also note this in the readme:

###Contact Any questions about the project please send email to: hjiang5 AT stevens DOT edu

mgradowski89 · January 14, 2019, 8:00pm

Ok It work, but:

$ ./CUDAMPF -msv 100.hmm Pfam-A.fasta 
Your input is: -msv
.fsa file open well
Got hmm length
In this database, we have 10626097 seqs.
The HMM size is 100.
msv:2
vit 2
.hmm file open well
MSV MU: -9.567800, LAMBDA: 0.717550
viterbi MU: -10.300500, LAMBDA: 0.717550
Forward MU: -3.482100, LAMBDA: 0.717550
.hmm file open well
.hmm file open well_trans
model process time: 5.002000 (ms)
.fsa file open well

 Total residue = 1651233608
.fsa file open well
the seq database has been aligned!!
whole seq database process time: 58470.171875 (ms)
WARP_SIZE = 32
SMX = 5
MAX_SMEM = 65536
========== MSV Filter ==========
SMEM MSV::warps per block: 32
SMEM MSV::resident blocks per SMX: 2
read .cuh file time: 15.221000 (ms)
Using SMEM: load in "SMEM_MSV.cuh" kernel file...
Available registers per thread is: 32
Alloc & H to D Copy time: 287.371002 (ms)
nvrtc Creat and Compile: 1028.665039 (ms)
Compile & Load time: 58.537998 (ms)
checkCudaErrors() Driver API error = 0702 "CUDA_ERROR_LAUNCH_TIMEOUT" from file <RTC_MSV.cpp>, line 181.

I Trying to reconfigure xorg.conf, but it reset ;/ and nothing happens

Robert_Crovella · January 14, 2019, 8:09pm

This is a completely different issue. Kernels running on a GPU that is hosting a display generally have a limit on runtime duration. You can confirm a runtime limit on kernel execution with the deviceQuery sample code.

Since you appear to be on linux, this may be of interest:

[url]USING CUDA AND X | NVIDIA

The best solution if possible is to make sure that Linux (i.e. X) is not configured to use your CUDA GPU for display purposes. Since you are on a 960M this may not be possible.

mgradowski89 · January 14, 2019, 9:17pm

So if I will use to display intel graphic problem will be solved? I tried for this change xorg.conf, but when i restart ubuntu xorg reset my changes