You can, of course, run mtr or traceroute on your own VPS in any Linode location.
Linode's Fremont location is Hurricane Electric's Fremont 2 data center; the
HE looking glass supports it (indeed, it appears to be checked by default).
As for Atlanta, that's at Zayo's AtlantaNAP data center. I don't know if there's an official LG, but a Linode customer (myself, as it happens) runs an
online mtr thing in Atlanta.
https://mtr-atlanta.mn0.us/?q=-bc+8+103.15.31.2Code:
$ mtr --show-ips -r -w -c 8 -i 1 103.15.31.2
Start: Fri Jul 10 07:33:39 2015
HOST: fairy Loss% Snt Last Avg Best Wrst StDev
1.|-- router1-atl.linode.com (64.22.106.73) 0.0% 8 0.5 0.5 0.5 0.6 0.0
2.|-- 64.22.106.9 0.0% 8 0.7 0.5 0.4 0.7 0.0
3.|-- atl-core-g-g1-6.gnax.net (63.247.69.178) 0.0% 8 0.4 0.5 0.4 0.5 0.0
4.|-- 7-1-7.ear1.Atlanta2.Level3.net (4.35.6.113) 87.5% 8 7459. 7459. 7459. 7459. 0.0
5.|-- ae-4-90.edge1.SanJose3.Level3.net (4.69.152.208) 0.0% 8 62.4 62.5 62.4 62.7 0.0
6.|-- ae-4-90.edge1.SanJose3.Level3.net (4.69.152.208) 12.5% 8 62.5 63.1 62.4 66.8 1.5
7.|-- 4.53.208.102 0.0% 8 62.3 62.3 62.0 62.6 0.0
8.|-- TenGE13-4.br01.hkg12.pccwbtn.net (63.218.174.61) 0.0% 8 198.2 226.8 198.2 344.4 54.9
9.|-- equinix.ge9-1.br01.hkg12.pccwbtn.net (63.218.175.2) 0.0% 8 201.5 198.7 198.2 201.5 1.1
10.|-- ge-1-2-9.gw1502.hk1.ap.equinix.com (27.111.175.187) 0.0% 8 214.5 218.8 214.5 247.9 11.8
11.|-- 202.167.235.102 12.5% 8 214.9 215.2 214.7 216.9 0.4
12.|-- 202.52.136.241 12.5% 8 221.6 223.9 221.5 234.9 4.8
13.|-- 202.167.235.38 12.5% 8 221.8 222.2 221.8 222.8 0.0
14.|-- suspended-2-31-15-103.MarchingSound.com (103.15.31.2) 12.5% 8 221.6 225.6 221.6 247.8 9.8
(The 12.5% loss on the last hops is probably due to an mtr bug fixed in later versions; it doesn't always wait long enough for the final packets to arrive.)
I'm not sure how much a couple mtrs or traceroutes will tell you about whatever your Internet issue is. It's probably with one of the ISPs along that route, or simply due to the distance involved, and there may not be anything that can be done.